Applied Freshwater Stream Ecology, Spring 2011
Copyright  2011 by Thomas Shahady, Lynchburg College
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Preface
This text is written for undergraduates taking my Freshwater Ecology Course. It is written through the inspiration of those students that constantly reminded me that the text was boring, not relevant, bad or otherwise. Now you have a text relating directly to the work we endeavor to do. I hope this text does not fall into previously described categories.
This current version is my first draft and will improve with constant revisions from the Freshwater Ecology Classes. I look forward to that endeavor and anticipate much improved versions to follow.
Acknowledgments
I want to thank the many students of Freshwater Ecology who inspired me to take on this task. I have so much support from family, and those around me that help to inspire. I hope this was worth the effort. And I also acknowledge the
School of Science at Lynchburg College providing me with the necessary tools to get the job done. Thanks.

I. The Applied Study of Freshwater Streams a. Why Study Aquatic Ecology b. The Water Cycle c. Human Pressures on a Key Resource d. Economic Considerations e. Key Words
II. Use of Applied Science in Freshwater Investigations a. Freshwater Scientific investigations b. Practice of Ecology c. Measurement and Scale d. Use of Science and Ecology in Freshwater Policy e. Key Words
III. Characteristics of Water a. Chemical b. Physical c. Biota d. Key Words
Characteristics of Freshwater Streams a. Watershed b. Characterizing Stream Habitats c. Hydrology d. Key Words
V. Chemical Characteristics of Streams a. Background b. Dissolved Oxygen c. Temperature d. pH e. Conductivity f. Alkalinity g. ORP h. Carbon i. Phosphorus j. Nitrogen k. Sulfur
Spiraling

VI. Biological Characteristics of Streams a. Background b. Periphyton c. Freshwater Macroinvertebrates d. Macroinvertebrate Groups e. Metrics of Water Quality
Fishes g. Characteristics h. Fish Functional Groups i. Index of Biological Integrity
VII. Ecological Characteristics of Streams a. Habitat b. Ecosystem Ecology and Stable Steady States c. Stability and Sustainability
VIII. Water Pollution, Improvement and Restoration a. Stormwater b. Stormwater Regulation c. Water Quality Improvement Through Restoration a. Simple Experimental Design b. Outline of Data Analysis

Why study aquatic ecology?
A thunderstorm builds and proceeds to produce a rain event pouring rain at a rate of 2 inches per hour. Typically during a rain event (less than 1 inch per hour) water is first intercepted by trees and plants adsorbing much of the energy of force from a raindrop starting its initial pathway into the soil. As this rain event continues, water infiltrates into the soil filling interstitial spaces and recharging groundwater. This groundwater is essential for recharging these streams throughout periods void of rain events maintaining the aquatic environment. .
Only when the soil becomes saturated or it begins to rain at rates greater than infiltration will water runoff over land into a stream. Water begins running over soil instead of through it and then collects into swales, conveyance, ephemeral, intermittent and eventually perennial streams (Figure 1). Where soil is disturbed erosion begins. Intensity of storm water carries with it proportional sized items into the stream. This may be soil particles, pollutants or trash. Understanding how streams function is very important.

Figure 1 – Ephemeral Channel

Figure 2 – Intermittent Stream

Figure 3 – A Perennial Stream in Central Virginia

The Water Cycle
Thunderstorms, rain and any precipitation event are portions of the water cycle.
The cycle (Figure 2) begins (or ends) over the oceans where evaporation creates clouds and water vapor in our atmosphere. Clouds through various meteorological events move over land and release precipitation in varied intensities and forms. It is in the precipitation where impacts to water resources occur.
In vegetated areas precipitation is intercepted before it hits the earth’s surface.
This interception is critical to prevent erosion and enhance

Figure 4 – The hydrologic cycle infiltration into groundwater. Trees provide the greatest rates of interception as precipitation contacts leaves, branches and tree trunks creating streams flowing down into groundwater. Other forms of vegetation provide interception of varied

effectiveness essentially dependent upon the ability to dissipate energy and create infiltration into groundwater.
In non vegetated areas precipitation almost instantaneously becomes runoff as it hits the earth’s surface. Denuded soil cannot infiltrate precipitation in a similar manner as vegetated land. Precipitation dislodges soil particles, and moves along the surface very easily following contours along the surface into swales, streams and rivers. Some of the precipitation will infiltrate but these rates are slow as soil becomes easily overwhelmed without vegetation providing pathways down through the soil. In fact soils high in clay content become less permeable for infiltration as they dry.
Areas with impervious surface do not permit precipitation to infiltrate. These areas of construction are built with conveyances to move receiving water from the impervious surface to some receiving body of water. Often the interface between these built conveyances and the area receiving the runoff very poorly and properly transfer this runoff to surface flow. Structures such as outlet protection and sedimentation ponds are designed to facilitate this transfer.
These structures are too often poorly maintained and ineffective in original design. What results is erosion and delivery of water volumes in excess of design and well above historical water volumes for these waterways.
Human Pressure on a Key Resource
Water availability and water quality are essential elements of the human environment. As population globally increases, continued pressure to obtain clean sources of freshwater will increase. It is important to understand that available sources of water must also meet minimum requirements of quality to meet human consumption needs. Interestingly, most river basins throughout the world face some level of impairment. In the United States fecal coliform impairments plague many of the waterways. As we are transferring much of the precipitation to runoff through the extensive development of impervious surfaces these same water supplies are being contaminated with bacteria and other pollutants. Increasing the supplies of potable water will be challenging field in the future.
Additional concerns exist for rivers and lakes unused for drinking water supplies.
Uses such as flood control, aesthetics and recreation build upon the assets of local communities and the livability the citizens enjoy. Real estate prices, the chamber of commerce, business development and jobs indirectly rely on the enhanced quality of streams and lakes throughout any community. To properly

protect these systems land use controls through zoning, community planning and conservation easements should be adhered to. The water quality of any stream and lake system is a reflection of the land use condition throughout the watershed.
Economic Considerations
Within any watershed land disturbing activity continually occurs. In rural communities this is predominated by agricultural activity. By contrast, in urban areas sprawl and urbanization are the dominant landscape features. It is important to understand that these activities are essential to maintain a vibrant economy, allow people to work and produce the communities we all would like to be part of. Too often, development is approached with only the concerns of ease of construction, maximum profits and traditional construction and engineering techniques. This approach interferes with the natural functioning of ecosystems, pollutes water and creates landscapes that are visually and ecological dysfunctional.
The idea that economic development and environmental protection cannot occur simultaneously is merely perceived. Many communities believe this to be true and therefore it becomes a self fulfilling prophecy. Data suggests environmentally sound development enhances communities, builds confidence and trust between developers and citizens and creates desirable communities.
Because water is such a valuable resource its protection should be at the heart of any development and community planning activity.
Because most communities have not followed sound environmental principles in development many areas are looking to techniques for water quality improvement and control. Previous regulations only demanded that water quantity be controlled in a development project. Further complicating this environmentally each project was only considered independently based on current conditions. Thus a mall or residential community needed to engineer only the amount of water running off its buildings and parking lots in the present condition and only based on a 10-year storm. The fallacy of this occurs when a new development occurs in the watershed. Ultimately, any change
(development) in the watershed simultaneously changes the current engineering for existing structures. So the existing mall or residential community engineering should be upgraded to reflect this new condition if we were to properly manage our development in our watersheds. This practice has not occurred and therefore degradation of our streams has followed.

New regulations have been developed to try and capture some of these problems. Stormwater is now regulated for both quality and quantity. This forces engineers to install features to treat the water before it is released into streams.
Communities are also looking for retrofits to fix many of the problems in
Stormwater that occur when communities are developed over 30-50 year time periods. Revenue to comply with these new regulations come from various sources. New project development now faces much higher costs to permit a project for environmental protection. Communities are raising taxes, utility rates and creating environmental fees to raise enough capital for this enhanced protection. Because so many years have elapsed without adequate protections it will take significant periods of time and revenue to fix many of these problems.
But while revenue is diverted to these projects the overall quality of life will increase due to the environmental improvements.
Key Words
10-year Storm – A storm of such intensity that it would only occur once in a ten year period. While this intensity is based on a statistical average multiple storms of this intensity may occur on a more or less frequent basis. It should also be noted that this intensity is based upon the watershed characteristics at the time of development and will change as the watershed is developed or reclaimed.
Community Planning – Process by which a local community determines how urbanization and urban sprawl should proceed.
Conservation Easements – A restriction placed upon the deed of a parcel of property preventing development and preserving the natural features.
Conveyance – area of water collection and transport.
Development Project – any construction such as a mall or house where land is disturbed and something is constructed.
Ephemeral Channel – water channel devoid of any permanence or connection to ground water. These channels are not legally protected under the Clean Water
Act.
Evaporation – conversion of liquid water into water vapor creating humidity, clouds and atmospheric forms of water while creating loss to surface waters.

Fecal Coliform – A group of bacterial living in the intestines of warm blooded creatures. Levels of this bacteria correlate with levels of pathogens in water dangerous to human health.
Impervious Surface – A surface such as pavement or a roof top that prevents water from infiltrating into soil.
Infiltration – The process whereas water moves from the surface into interstitial spaces in the soil creating groundwater.
Intercepted – process where precipitation contacts vegetation before hitting the ground aiding in transport and infiltration to groundwater.
Intermittent Stream – water course connected to groundwater during wet seasonal periods. These channels have legal protection under the clean water act.
Outlet Protection – engineered structures designed to dissipate water flow and prevent erosion as it leaves a pipe or parking lot.
Perennial stream – water course continually flowing throughout the year and connected to groundwater throughout the year. They are legally protected under the Clean Water Act.
Potable – description of water indicating that it is safe to drink.
Regulation – rules pertaining to law that prescribe how an individual or entity should behave to be in compliance with the law.
Retrofits – reengineering an existing development project to properly process
Stormwater due to changes in the watershed or lack of proper engineering on site.
Runoff – process where water either through saturation of soil or placement of impervious surface flows over land and into a water course.
Sedimentation Pond – engineered structure designed to restrict the flow of water from an area of construction.

Sprawl – the uncontrolled growth of development usually consisting of chain retailers, fast food restaurants and undesirable traffic conditions.
Stormwater – water runoff generated from precipitation during storm events.
Swales – depressions or topographical features creating the collection and transport of water.
Urbanization – development of land consisting of buildings, road networks, sewers and other human amenities.
Water Quality – The measured levels of pollutants or other inhibitants in water.
Water Quantity – The measured level of water flow and volume.
Watershed – the collective basin encompassing a network of streams, lakes or other features.
Zoning – legal classification of land indicating the intended use within a community.

Freshwater Scientific Investigations
Science can be defined as the study of natural or natural phenomenon. In the study of freshwater ecosystems we need to use science to establish things such as degradation, contamination and stream or lake condition. We do not want to confuse this effort with policy. We often interject our scientific findings into policy to affect change or protect water resources. It is critical to separate how we conduct scientific investigations and how we approach policy to affect change.
In our approach to study the water quality of freshwater resources we act essentially as detectives. We have a stream interconnected with the land and connecting further with lakes or other streams eventually flowing into the ocean.
We want to understand the quality of this stream and begin to investigate all available information we can collect. We collect, question, revise our ideas and come to conclusions only with the data we have available. We are using the scientific method.
The scientific method describes what we know as a cycle of knowledge accumulation. While scientists may approach investigations in differing ways, all follow steps in the scientific method that calls for the constant refining of knowledge though experimentation, peer review, repetition and critical analysis.
When conducting investigations of water quality it is important to adhere to the scientific method.
The use of reasoning also is critical in investigations. Two types of reasoning are used: inductive and deductive. When we induce a conclusion we base this upon our empirical observations collecting data and facts thus drawing conclusions.
We collect data showing that a stream has high concentrations of a pollutant so we then induce that the stream is polluted. But we must be careful. These conclusions often contain some form of observational bias. As a scientist we should study a stream to document its quality and use our induction to both report findings we set to determine as well as findings that do not support our hypotheses. If I observe a stream and believe it to be polluted then often my investigation is designed to demonstrate that it is polluted. This is a biased approach and if we do not find the evidence for pollution we sometimes will not report this negative result. It is always important to report both positive and negative findings in science. Finally, using induction and the scientific method we can develop laws and theories about the phenomenon we are studying.

Deduction is, unlike induction, the use of observation and logic to extend conclusions beyond what was observed. Deduction allows us to develop predictions and explanations beyond what we have directly observed. When we find that a stream has become polluted due to development of a large mall or subdivision we can deduce that a mall or subdivision in other communities will be polluted also. We do not have the direct data to demonstrate the streams in other communities are polluted but using logic we can reasonably assume they are. At times deduction may lead to inaccurate conclusions. Understanding that species of darters eat mayflies and stoneflies we may deduce that without these insect species in a stream darters will not be found. This deduction may be incorrect as the darters may switch to alternative prey or coexist with these species to the point we do not find stoneflies and mayflies in the stream. When we deduce we must be careful with our conclusions. However, deduction often leads to breakthroughs in our understanding of the environment.
Another tool we may use in our investigations is strong inference. Inference leads us to a conclusion we believe to hold true even though much of the supporting data is circumstantial. As we measure stream water quality we discover a very high level of phosphorus. We then conclude that this steam is being polluted by nutrients and infer that nitrogen is elevated also. Here we may be deducing this conclusion as well because we do not have any nitrogen data at all. But knowing that elevated phosphorus concentration always accompany elevated nitrogen concentrations we can use strong inference to conclude this stream has elevated nitrogen as well.
One final thought as look at the role of science in the study of freshwater. Do we rely too much on science or should there be a separation of science and state
(for more on this topic read Feyerabend Against Method or Science in a Free
Society). In some instances this can be argued. Science is a tool in a toolbox and does not provide the definitive answers to our questions. Is a stream polluted? We can provide ample evidence showing elevated pollutants, degraded stream banks and poor aesthetic quality and yet the stream may having a thriving population of fish. Sometimes even the most vigorous science cannot capture the essence of sitting next to a waterfall or enjoying ducks swimming on a pond. To only rely on science to drive our decision making results in a loss of some of our power as human beings.

Practice of Ecology
What is Ecology? Ecology is the study of organism integrated into their environment. How does the study of freshwater rely on ecology? It is integral to our study of freshwater because ecological relationships dictate the natural phenomenon that we observe and measure. Concentrations of dissolved oxygen in water are impacted by the exchange between water and the atmosphere. But this explanation is only a small portion of the dynamics between oxygen and water. Photosynthesis and respiration drive the over-abundance or underabundance of oxygen and distribution and abundance of the organisms responsible is driven by ecology. It is therefore critical that we have some understanding of basic ecology as it applies to freshwater ecosystems.
The basic unit of ecological study is the organism. In freshwater we study abiotic impacts such as temperature, pH and oxygen on the organism. The next unit of study is the population. This is a group of organisms or species living together in the same place at the same time. Areas of study include population growth and regulation. Next unit of study is the community. Communities are groups of populations interacting in the same area. Areas of study are competition and predation. And then we have the ecosystem. Ecosystems are communities interacting with the surrounding environment. We typically study emergent properties and large scale interactions in ecosystems.
Another important concept in ecology is the niche. The niche describes the functional role of an organism in an ecosystem. This would include its range of tolerance, resource use, species interaction and flow of energy. Often niche is used in our study of freshwater to describe what an organism does such as an omnivore or pool benthic carnivore. Other instances we may group multiples of organisms and populations into similar trophic levels or guilds to describe what they do. Scraper or collector are terms often used to describe insect life in streams.
Habitat describes where an organism lives. It is important to understand that resources within habitats are often clumped creating patchiness in the distribution of organisms. Adaptation is the fit between the organism, their niche and habitat. Thus when looking at the distribution of organisms along a resource gradient we typically find the best adapted species for the conditions existing at this time. It is very important to consider niche and habitat when conducting biological surveys for water pollution. Absence or presence of certain indicator species may solely arise from differences or similarities in habitat and niche and have no relevance to pollution impacts on the stream.

Trophic structure is the organization of similar populations into organized levels of construction. Typically in a freshwater ecosystem we find the following organization (Table 1). Each level serves to provide energy to another level with the sun through photosynthesis providing the initial energy to the system. Most interactions are aerobic using oxygen to convert organic nutrients back into CO
2 and water. Alternatively organisms may use anaerobic respiration – in absence of oxygen breakdown into methane, ethyl alcohol, acetic acid and hydrogen sulfide. Certain species of bacteria can use this form of respiration during periods of low oxygen.
Trophic Level Description Examples
Producer Phytosynthetic Algae, Phytoplankton,
Herbivores
Organisms
Grazers and Filter
Feeders
Macrophytes
Zooplankton, Insects, Fish
Carnivores
Secondary
Carnivores
Omnivores
Detritivores
Meat eating Organisms
Plant and Animal Eaters
Detritus eaters
Decomposers Decompose matter
Birds, Mammals, Fish
Crayfish, fish, birds, mammals
Fish, insects
Bacteria and Fungi
Scavengers Eat dead or dying organisms
Birds, insects
Scientific studies in ecology are done in many differing ways. Some are explanations of natural history. These types of studies describe the life cycle of organisms from reproduction to growth of populations. Such studies help us understand how, where and why organisms are distributed as they are. Another type of study is empirical surveys. These studies collect data on a variety of systems and correlate the results to look for patterns and relationships in nature.
These types of studies are excellent from the perspective of mimicking the natural environment but very poor in terms of experimental protocol and reproducibility. Experimentation is the corollary to empirical surveys. Dependent and independent variables are manipulated to derive an experimental result often in a laboratory or manipulated field site. These types of studies give us understanding of relationships in nature and cause and effect but are often criticized as an oversimplification of the natural environment.

Measurement and Scale
Two additional measures of ecology are important in our study of freshwater ecology. To understand both the how organisms are distributed and the seasonality of these distributions we must understand patchiness. Patchiness describes how organisms tend to clump around resources.
Scale is our other measure of interest and can be described within both space and time. It is important to understand that ecological investigation typically looks to describe and understand the patterns we see within a scale. If we measure the density of mayflies in a stream we may wish to compare that density with another stream elsewhere on the same day or even at another place in the same stream. This investigation is looking at changes with respect to space. We then make some conclusions about the relative health of the stream based on these differences. What is good about such comparisons with respect to space is that seasonal and weather factors are identical and therefore our inferences can be based on the differences between the two areas we have sampled. The limitations of these comparisons relates to the differences in the areas such as flow, watershed characteristics and pollution levels that impact the stream and we cannot control. This is way we additionally make comparisons in time.
Time comparisons represent studies of an area through successive years. This allows us to look at how the system changes and responds to changes that may occur to the surrounding area or simply look at the natural variation in the area.
What is good about these comparisons is that we have true replication of our sampling because we are sampling the same system at the same spot with only changes in the surroundings to correlate to changes we find in our samples. The weakness lies in the seasonal changes that occur year to year that we cannot control for. Therefore it is often desirable to blend both types of studies and make our conclusions based on the strengths of each type study while also recognizing the limitations.
Resolution represents the size of our samples (space) or period of time (time).
Increasing the resolution increases the strength of the inference you are making.
Range describes the total size of examination or total time of sample. Scope is the ratio of total area or time sampled to our individual area or time sampled. So how do we determine the optimum sample size or what is our ideal resolution?
How does it relate to our experiments? What about spatial and temporal resolution? What is the importance of scale?

Many of these questions can be answered statistically. Whenever we state that one condition is different or the same as another condition we use statistics to substantiate that claim. Therefore, optimum resolution or sample size is dependent upon the claims we are making. If we want to determine if a pollutant is creating a change in a stream we often need a minimum of three samples to create a mean and a standard deviation or variance. When the mean of our measurements exists with relatively little variation this creates more power in the comparisons and usually produces true differences. It is important to understand statistics and their proper use in science.
Use of Science and Ecology in Freshwater Policy
One of the interesting political divides in the management of freshwater resources is between fisheries and water quality professionals. Water quality professionals work under EPA in state programs and are focused primarily on pollution. They may use biological indices to predict water quality but the focus is typically on pollutant degradation not ecology. This is not to imply these scientists and administrators are not trained in ecology. Fisheries biologists work under the equivalent of the Department of the Interior at the state level are focused primarily on fisheries management. These biologists are trained in ecology and approach fisheries management ecologically. They may show concern for water quality but only when it impacts the ecological management of fish populations.
The difficulty with this approach comes within a stream or a lake. While fish populations and water quality are managed independently politically, they are intertwined and hopelessly interdependent in freshwater ecosystems. When a fish kill occurs it can be the result of many factors but most likely is due to a dramatic loss of oxygen. What agency is responsible? Well, because it is a water quality issue it is the responsibility of the state EPA. But it is the fisheries biologists who have the expertise to identify and determine the impact to fish populations. So now an environmental problem that needs resolution involves two state agencies cooperation and has become more difficult to resolve because of policy. Do we have access to information from both agencies? Do we have enough agents?
1. Can good science direct policy? Is sediment good or bad for streams – burrowing vs. surface feeding insects and fish?
2. How should science be used in directing policy – compromise or deflect ideas? Allow development or prevent it?

3. Can Science provide a solution or does it tend to wedge people apart?
Science is not set up to provide absolutes and therefore can be manipulated in favor of individuals – it often provides a wedge.
4. Separation of science and the State? – Is it the final answer to our problems or do other disciplines – religion, arts provide a better basis for environmental protection?
Key Terms
Bias – alternative conclusions draw from similar data based on presuppositions of the investigator.
Biological Indices – created scales using indicator species providing a measure of water quality.
Circumstantial – evidence supporting a finding or theory not directly related to the finding or theory.
Community – Populations interacting in the same place at the same time. Two primary population interactions of study is competition and predation.
Correlate – the practice of predicting a result using another measured variable.
These variables are described as dependent and independent.
Department of the Interior – is a federal agency charged with protection of natural resources mainly wildlife and parks. While this department does not have jurisdictional authority over state departments charged with the same policy they do maintain the National Fish and Wildlife Service charged with protection of federally endangered and threatened species. In Virginia this agency is DGIF or
Department of Game and Inland Fisheries.
Dependent variable – the variable of change based on the dynamics of the independent variable. By adding phosphorus (independent variable) to water we often see increased growth in phytoplankton (dependent variable).
Ecosystem – Interaction of biological (biotic) communities along with the non biological (abiotic) components. Examples are a pond, stream or forest.
Emergent Properties – properties of ecosystems that develop only on the ecosystem level. The stream bed is an emergent property developing out of rocks, mud and woody debris.

Empirical – data collected through observation as opposed to theory or conjecture.
Empirical Survey – study of patterns in nature using observations collected in time and space.
EPA – Environmental Protection Agency is a federal agency charged with protection of the environment and organized at the state level for implementation of this policy. In Virginia this agency is DEQ or Department of Environmental
Quality.
Experimentation – use of scientific process to to discover process and patterns in observed phenomenon.
Fish Kill – event where fish are killed in a pond, lake or stream. Most fish kills are a result of low oxygen in water other than a toxic spill.
Habitat – The physical space occupied by populations. Rocks, twigs and leaves all provide habitat for aquatic organisms.
Independent variable – the variable of change that is independent of the dependent variable. Phosphorus additions (independent variable) to water occur regardless of the increased growth in phytoplankton (dependent variable).
Inference – use of data to develop a reasonable conclusion based upon that data. Inference is not necessarily directly supported by the evidence but indirectly supported.
Logic – process for developing a conclusion using a sequence of related events.
Logic is most often used to provide working theories.
Mean – the average measure from observations or experimentation.
Natural History – Detailed description of the life cycle for an organism.
Niche – The functional role of an organism in an ecosystem. Typically related to feeding such as a benthic omnivore or water column producer.
Organism – Individual species identifiable through reproductive isolation

Patchiness – the observation that organisms tend to clump around resources and are not evenly distributed.
Peer Review – process where your scientific colleagues read and critique your science before it is published in the scientific literature. This is critical to maintain the integrity of science.
Policy – documentation of how government interacts with issues and the public.
Population – Group of organisms occupying the same place at the same time.
Scale – degree of refinement in your measure. Findings are often dependent upon the scale of measure.
Scientific Method – The methodology used by scientists to investigate natural phenomenon. It consists of asking questions, forming an hypothesis, conducting experimentation, analyzing results, drawing conclusions and then repeating the process to strengthen or refute our hypotheses and questions.
Space – observations of measures along differing areas of a landscape.
Statistics – mathematical measure used in ecological investigations to describe changes or differences among populations, measures or scientific experimentation.
Standard deviation – the measure of error in our investigation.
Steps in the Scientific Method
Observations – patterns or problems
Explanations – models, theories and metrics
Hypotheses and Predictions
Tests of Models and Predictions – Tests and Controls
Deductions and Inductions
Inherent Variability - noise in experiments and tests
Time – observations of measures along differing times in a landscape.

Chemical
Water is comprised from the elements hydrogen and oxygen. Water is formed into a molecule through a weak bond of hydrogen and oxygen. Also comprising water are ions of hydrogen (H + ) and hydroxyl (OH ).
H H
O
Figure 1 – Water Molecule
This gives water several unique characteristics. First, water develops its greatest density at 3.96 degrees C and has a density of 1 gram per cm density of 0.917 grams per cm 3
3 . Ice has a
allowing it to float in water at any temperature.
This creates an environment where water will layer into stratified sections.
Figure 2 – Density (Kg/m3) of water at various temperatures (C). The greatest density is found at 4C.

Secondly, the solubility of gasses (ions) decreases with temperature. This affords water the ability to hold gasses in solution for extended periods of time with oxygen and carbon dioxide being of great importance. For example, as water heats the concentration of important gases decreases (figure).
4
3.5
3
2.5
2
CO2
O2
0.08
0.07
0.06
0.05
0.04
1.5
1
0.5
0.03
0.02
0.01
0
0 10 20 30 40
Temperature of Water (C)
50 60
0
Figure 3 – Solubility of oxygen and carbon dioxide in water of varying temperature.
Water has additional unique properties including:
 High heat capacity – resists temperature change
 High heat of fusion – resists freezing
 High heat of vaporization – resists becoming a gas
 High surface tension – resists mixing with air
Conceptually thinking about water we could say water tends to stay in a liquid form and resists change. In other words, it does not want to change and wants to be left alone.
Physical
The physical properties of water create an environment unique to the organisms and chemistry in water. As was stated previously the makeup of water makes it

resistant to change. The same is true of viscosity. Water tends to resist changes in viscosity but these changes occur as water temperature and hence water density change. Colder water is more viscous. This creates changes in how water flows around objects and how organisms are impacted in movement.
Greater viscosity creates greater attractive forces relative to the organism.
Levels of viscosity impact the flow of water as more viscous water creates a greater sheer on its surrounding environment and the organisms in the water.
This increased sheer slows down water movement and impacts the inertia of water. Inertia describes the resistance to a change in motion and increased viscosity also increase the inertia of water. Once overcoming inertia the water possesses greater momentum and takes more energy to stop. This creates a phenomenon of sheer stress that physically pushes debris and organisms down river. Biota are adapted to varying levels of sheer stress.
When describing the condition of water relative to inertia and viscosity we can assign a Reynolds Number. The Reynolds number (Re) is dimensionless and it helps us to understand how becomes more viscous (or thicker) with flow. When
Re exceeds a critical value (usually between 500 and 2000) the water flow becomes turbulent. Below this value we have laminar flow. It will change due to a multitude of factors such as size of river, scale of measurement and flow rate of the water.
Types of Flow
Water flow is generally described as laminar or turbulent. Laminar flow is ordered, homogenous, unidirectional, and increases toward small scales because viscosity increases. It is typically quiescent and uniform. With increases in viscosity, flow rate and friction - flow evolves to turbulent. Turbulent flow is unpredictable and creates vortices, wakes and eddies. This type of flow is disruptive to stream ecosystems often scouring stream bottoms and eroding banks. Turbulent flow is the rapid movement of water creating eddies and other characteristics of rapid movement. It decreases toward small scales but is the predominant condition of water flow during storm events.
All flow that occurs near solid surfaces creating a boundary layer. The boundary layer is a quiescent area of water between an object surface and laminar flow. It is extremely important for the survivorship of many aquatic macroinvertebrates.
Boundary layer thickness changes with the surroundings. Thickness decreases with increased velocity of water, decreased roughness on the surface of the

object, decreased distance from upstream edge of an object and decreased size of object. These properties make it advantageous for an organism to live in certain habitats dependent upon flow conditions and habitat.
Boundary Layer
As water flows past an object a boundary layer appears.
Zero Velocity Layer
Surface
Figure 4 – Boundary layer creation over solid surface under turbulent and laminar flow. With laminar flow velocity becomes zero and with turbulent flow velocity becomes unstable creating eddies and scour.
Within the boundary layer diffusion becomes very important. Chemical movement such as oxygen and nutrients moves freely through the boundary layer providing nutrition to both plant and animal life. Molecules are transported through Brownian movement and diffusion predominates. Upon the development of turbulent flow, eddies destroy the boundary layer transport and nutrition of organisms in this layer.
Heat and Light
The penetration of light into water serves two purposes. It drives the photosynthetic apparatus of plant life to support the aquatic ecosystem.
Additionally, it heats the water.
Heating of water is related to intensity of light. On the water surface heats where light intensity is greatest warming occurs rapidly. With warming changes in density begin with less dense warm water occurring over more dense cooler

water. As this process continues without any inhibiting physical force the water will stratify. This creates an upper epilimnion of warm water floating upon a lower level of cool water in the hypolimnion. As wind blows upon the surface of the water and forces mixing only the epilimnion is mixed. This pattern continues until either cooling or physical flow of water breaks up this stratification. This is a common occurrence in reservoirs. Streams do not stratify because the water is in constant movement.
Streams are considered isothermal within a single reach at any given time due to mixing. Each can experience diel fluctuations in temperature. Headwater streams very constant in temperature – tend to see increase in temperature with stream length. This pattern is opposite in tropical systems. Riparian vegetation influences temperature and freezing impacts biota in systems where entire stream freezes.
The visible light spectrum are the wavelengths that are visible to the human eye.
These are the wavelengths that impact the color of water, organisms and other phenomena we observe. It also serves as the wavelengths of light used by plant life in water. Many species are adapted to take advantage of multiple wavelengths using various forms of chlorophyll or other pigments for adsorption of light.
Table 3-1 – Visible light spectrum
Red 625-740
Orange 590-625
Yellow 565-590
Green 520-565
Cyan 500-520
Blue 435-500
Violet 380-435
Light entering water is transmitted, absorbed and reflected. Particulates in water tend to reflect light preventing the absorption of longer wavelengths in water such as red and orange. Hence the water appears brown in these instances from sediment and particulates. Plants tend to absorb red and blue light and reflect green. Water absorbs the red and orange light and will reflect blue. Turbid water appears brown, water with abundant plant life appears green and water without particulates or algae appears blue.

As light further penetrates into water we get attenuation or loss of light with depth. Extinction coefficients provide us with a measure of productivity and materials in water. As productivity increases the extinction coefficients become greater.
Plant biota are very sensitive to light wavelength and penetration into water and have evolved apparatus to capture light in order to photosynthesize.
Photosynthetic pigments contained in chloroplasts in eukaryotes, and throughout the cytoplasm in prokaryotes (such as blue-green algae) absorb light to metabolize and grow. Chlorophyll is the molecule that absorbs the sunlight and all phytoplankton contain chlorophyll a that absorbs red and blue light. Others contain b, c1 and c2 with accessory pigments such as phycobilins (blue-greens),
- light antennae (allows adsorption in green window) accessory pigment to Chl a
Carotenoids - xanthophylls and B-carotene increase spectrum of light adsorption
– uv and blue light .
Key Words
Boundary Layer – layer in flowing water where there is no movement along sold surfaces.
Brownian Movement – random movement of particles suspended in water.
Chlorophyll – photosynthetic pigment used by plants to create simple sugars from sunlight and carbon.
Diel – day and night
Diffusion – movement of molecules from areas of high concentration to areas of low concentration.
Elements – the basic building blocks of all matter and each is contained in the periodic table of elements.
Epilimnion – the upper layer in a themally stratified lake or reservoir.
Extinction Coefficient – measure of the strength of absorption of light at a given wavelength.

Hypolimnion – the lower layer in a thermally stratified lake or reservoir.
Inertia – the momentum created by movement of water and responsible for things like eddies and turbulence.
Ions – a positive or negative charged molecule. Some common ions we work with are ammonium NH4 + , hydrogen H + , and hydroxyl OH -
Isothermal – iso is the term for similar and thermal describes temperature so an isothermal stream is the same temperature from top to bottom.
Laminar Flow – flow of water without disruptions
Molecules – combinations of atoms from two or more elements.
Reynolds Number – measure of the ratio between inertia and viscosity. Low numbers occur when water is viscous and laminar and high numbers suggest the water is turbulent with high inertial properties.
Sheer Stress – force applied from the movement of water.
Stratify – the separation of a lake or reservoir into thermally isolated layers.
Turbulent Flow – disruptive flow of water.
Viscosity – the resistance of a fluid or ability to flow. Honey has greater viscosity than water.

Watershed
Watersheds are the common divisional boundaries for studying streams and lakes. A watershed is the land surface area that a river system drains. We can determine these divisional boundaries by determining drainage patterns on slopes leading to a particular river or stream. All sizes of upland ridges contain the upper most boundaries for watersheds with precipitation runoff flowing off either side creating the unique watershed boundary. The valley floor will contain the rivers and streams that drain the land cover creating the watershed.
Interestingly, many roadways are built upon the upland ridges and sewer lines along the valley floors.
Figure 4-1. A watershed showing differing land use.

Watersheds or catchment basins begin along ridge lines directing water into terrestrial valleys eventually forming a network of streams entering the ocean. In the headwater area colluvial deposits formed by large land masses create the landscape. These areas are seldom moved through large episodic flooding events. In open areas springs and seeps create the beginnings of a stream system. Often these areas are wetlands. As water continues to flow downhill it becomes channelized first into ephemeral and later into intermittent streams as it gains a groundwater connection. Alluvial sediment and material begins to build up developing a perennial stream.
In confined systems very little floodplain exists on either side of the stream.
Otherwise a floodplain occurs on one or both sides of the stream in a unconfined stream system.
As we move from the headwater mountainous terrain into the coastal plain flat lands streams contain certain characteristics. In the mountain headwaters we find cascade reaches. Here the stream system consists of a series of waterfalls with a large hydraulic gradient creating riffles. This system produces heavy sediment removal and deposit into the lower reaches. The next system is steppool. Here, course substrata and small width to depth ratios create high gradients and flow rates. This system is not the gradient of cascade reach as the water slows into pools but nonetheless has very high stream velocities. Moving into the Piedmont regions we find pool-riffle-run system. This system is characterized by an undulating stream bed along with predictable pattern of pools, runs and riffles with sinuosity. Finally, as alluvial deposits build we find a braided stream system in the costal plain. These systems have large volume, slow velocities and continual lateral movement of the sediment bars.
Streams in any of these regions impacted by anthropomorphic development take on characteristics of the braided system. Large influxes of water volume and alluvial deposits create highly eroded stream banks with continuous sediment transport. In the piedmont streams become braided and highly unstable delivering large quantities of sediment with each storm event.
Characterizing Stream Habitats
Lotic environments can be approximated by streams order (figure 4-1). Any headwater channel, ephemeral or intermittent that contains water only during periods when evapo-transpiration is lower than precipitation will be classified as first order. Additionally, any perennial stream fed by permanent springs or otherwise with flow all year without tributaries is classified as first order. A first

order stream must originate without any tributaries. Now, to continue to classify a stream of second order occurs by convergence of two first order streams. A third order stream occurs by convergence of two second order streams and so forth. When a stream of any order intersects a stream of lesser order it remains unchanged. It is only when streams intersect of the same order does the order increase.
1 1 1 1
2 2
3
Figure 4-2 – Stream Order
Using the classification system we can generalize stream habitat according to stream order. First through third order streams contain channel beds at the level of groundwater. Water is cool, fast flowing and shaded by heavy forest cover.
Heavy inputs of allochthonus materials such as detritus, leaves, twigs, bark, and pollen fill the stream bed and are evident year round. The riparian buffers are well developed.
These lower order streams contain alternating riffles and pools. Stream beds covered in coarse stones and stones kept free of silt and sand by rapid water flow. These spaces between rocks are well oxygenated and provide critical habitat for stream organisms. Large cobbles and woody debris create stability generating leafpacks behind these obstructions. Course particle chewers called shredders consume the leaves described as Coarse Particulate Organic Matter
(CPOM). What shredders cannot consume becomes Fine Particulate Organic
Matter (FPOM) and what these organisms excrete becomes Dissolved Organic
Matter (DOM). This material becomes a food source for organisms in higher order streams.

Fourth and fifth order streams provide the transition between lower and higher order stream habitats. The channel bed deepens and widens. Flow is rapid with less developed riparian zones. The stream widens allowing sunlight onto the stream bed. Autochthonus inputs such as algae and higher plants grow and contribute new habitats and new types of food.
In fourth and fifth order streams the alternating riffles and pools also include runs.
Stream beds are covered in stones yet silt and sand begin to accumulate because of decrease water velocities. Riffles provide well oxygenated habitat between rocks while runs offer a silt and sand bottom for burrowing organisms.
FPOM is a primary food source and these organisms further produce DOM.
When canopy does not cover stream, algae and grazers such as snails cover rocks.
Pools provide a unique habitat for organisms in these lower order streams. Here we have slow-flow conditions with the bottom covered in sand and silt. These areas are poorly oxygenated during periods of low flow and the bottom sediments provides habitant for many organisms. Most organisms burrow in sediments to remain safe and out of site while various fishes forage into pools at night. These pools are essential refuges during summer months when flow rates are so low that riffles and runs are inhabitable.
Sixth through twelfth order streams are quite different than their lower order counterparts. The channel gradually becomes very deep and wide. Sunlight no longer penetrates to the bottom supporting attached algae. Flow becomes slow, bottoms very sandy and plants no longer rooted in system. Fine suspended detritus and attached algae from upstream become primary food source. As order increases, lentic conditions occur with phytoplankton as the primary food source.
Runs or reach become major habitat feature in these high order systems.
Sandy, silty bottoms provide the primary habitat for benthic organisms. Other organisms dwell upon snags such as tree limbs, trunks or other debris. Bivalves collect interstitial particles of detritus for food. In the mouth of rivers flow slows and vegetation occurs.

Figure 4-3 A third order urbanized stream
Hydrology
Stream discharge (measured in cubic feet per second or cfs) is a function of stream morphology and watershed size and characteristics. Watershed that are thin (figure 4-6) tend to have greater velocities of water through the watershed, shorter residence times and greater sediment transport than watershed that are wide. Material transported by streams may be in solution as dissolved solids or suspended as suspended solids. With each storm this material is moved and subsequently deposited down stream. Bed load is the heavy sediment deposits that are only displaced and moved during large storm events. Sedimentation is the material that is transported down stream during every storm event.

Figure 4-4 – Differing shapes of watersheds.
Stream channel morphology describes the characteristics of the stream. The thalweg is the deepest, swiftest section of the stream. The stream channel is the area of continual water flow while the stream course includes the floodplain. The sides of the channel before intersecting the floodplain is considered the bankfull depth. How much the stream meanders is considered the sinuosity.
Entrenchment is scouring of the stream channel during storm events and measures the impact from storms. The width to depth ratio measured as the

bankfull width to bankfull depth or floodplain width to bankfull width provide measures of this stream characteristic.
Stream bottoms are classified by the bed material. Bed Material may be
Bedrock, Boulder, Cobble, Gravel, Sand and Clay. All are classified depending on size. Pools are characterized by shape and function. We have pool, plunge pool, lateral scour pool, backwater pool, dammed pool and glide. Riffles are characterized by flow and substrate. We have riffles, rapid, cascade, side channel and falls.
Hydrographs describe river discharge over time. Flow is denoted by Q and storm intensity by the number. Hence a one year storm is denoted by a 1 and a ten year storm a 10. Thus a hydrograph for a 10 year storm is described as Q10.
Storm intensity must be understood here. A ten year storm is the predicted rainfall for a storm that should occur once every ten years. The rainfall event would occur over a 24 hour period and produce flow rates in a stream based on the amount of precipitation intercepting a certain land use. Ten year storms may happen in subsequent years but then we would expect the next storm to occur in the next 20 years.
Assessment of the physical stream condition occurs using the Unified Stream
Methodolgy developed by both the US Army Corps of Engineers and Virginia
Department of Environmental Quality. This methodology is a good starting point in scoring streams physical condition and gives a relative score for comparison.

Key Words
Alluvial – deposits of sediment and rocks transported by the flow of water.
Allochthonus – input of energy from external sources such as leaves from trees
Autochthonus – input of energy from internal sources such as periphyton growth on rocks.
Benthic – bottom dwelling
Braided – sand bar development in streams
Cobbles – rocks of characteristic size lining stream beds
Colluvial – deposits of sediment and rocks transported by terrestrial processes such as land slides or earthquakes.
CPOM – Course Particulate Organic Matter
Discharge – measure of stream flow and volume as CFS.
DOM – Dissolved Organic Matter
Entrenchment – situation where a stream because very channelized
Floodplain – part of the stream course
FPOM – Fine particulate Organic Matter
Headwater – Stream at the origin of a system
Lentic – standing water system
Lotic - flowing water system
Morphology – physical nature of a stream or watershed
Pebbles – rocks of particular size along a stream bottom
Pool – areas of deeper slower moving water in the stream system.

Residence times - length of time it takes a drop of water to travel through a watershed
Riffles are shallow with fast, turbulent water running over rocks.
Runs are deep with fast water and little or no turbulence
Pool – Riffle – Run - typical stream sequence found throughout the piedmont areas. In a health stream this sequence should occur every 5-7 channel widths.
Reach – area of stream for study that is typically 20-30 times the width.
Riffle – area of fast flowing oxygenated water in a stream
Riparian buffers – tree lined area along stream banks
Run – area of fast moving water in stream
Sand – small particulate on stream bottom
Silt – fine sediment along stream bottom
Sinuosity – describes the meandering of the stream and can be measured as the ratio of thalweg to straight-line distance
Tributaries – any stream entering a watercourse
Watersheds – the catchment area of a river system

Background
Water chemistry is the first measure to assess the general quality of the water in streams. These measures are generally easy to obtain and give information that can be quantified and compared among streams and over time. It is important to remember these measures provide a “snapshot” of water quality in the stream.
You are sampling the water flowing through the stream at this particular time.
While the quality of the water you measure here is reflective of the water quality in the stream it does change over short periods of time.
Dissolved Oxygen
Dissolved oxygen (DO) is the concentration of oxygen in the stream water. It is measured either as mg/L or percent saturation. Percent saturation reflects the amount of oxygen in the water relative to temperature. As demonstrated in figure
5-1 water will hold a given amount of oxygen at that temperature. We define these figures as 100% saturation. Warmer water holds less oxygen than cool water.
Table 5-1 – Oxygen saturations for water at a given temperature.
Temp (c) DO (Mg/L) Temp (c) DO (Mg/L)
0 14.60 14 10.52
2 13.81 16 10.07
4 13.09 18 9.65
6 12.43 20 9.07
8 11.83 22 8.72
10 11.27 24 8.40
12 10.76 26 8.09
The stream system both produces and consumes oxygen. It gains oxygen from the atmosphere and from plants as a result of photosynthesis. Running water, because of its churning, dissolves more oxygen than still water, such as that in a reservoir behind a dam. Respiration by aquatic animals, decomposition, and various chemical reactions consume oxygen. This impacts the saturation levels.

In a system where production exceeds loss the saturation rates will exceed
100%. In systems where consumption is greater the saturation rates are less than 100%
Dissolved oxygen is measured either in milligrams per liter (mg/L) or as percent saturation. It is best to record both measures when sampling in freshwater.
Decisions on use of each measure are dependent upon comparisons of data.
Where multiple ranges of temperatures are involved in the study percent saturation is a better choice as this measure incorporates changes in temperatures and normalizes the data. When it is valuable to show absolute concentrations of oxygen in the stream mg/L is a good choice.
DO levels fluctuate seasonally and over a 24-hour period. They vary with water temperature and altitude. Cold water holds more oxygen than warm water and water holds less oxygen at higher altitudes. Aquatic animals are most vulnerable to lowered DO levels in the early morning on hot summer days when stream flows are low, water temperatures are high, and aquatic plants have not been producing oxygen since sunset.
Oxygen Cycling
In contrast to lakes, where DO levels are most likely to vary vertically in the water column, DO in rivers and streams changes more horizontally along the course of the waterway. This is especially true in smaller, shallower streams. In larger, deeper rivers, some vertical stratification of dissolved oxygen might occur. The
DO levels in and below riffle areas, waterfalls, or dam spillways are typically higher than those in pools and slower-moving stretches. If you wanted to measure the effect of a dam, it would be important to sample for DO behind the dam, immediately below the spillway, and upstream of the dam. Since DO levels are critical to fish, a good place to sample streams is in the pools that fish tend to favor or in the spawning areas they use.
Table 5-2 – Typical Aquatic Life Standards
Dissolved
Oxygen Minimum
Criteria
(mg/L)
7 Cold Water Spawning Species
6
5
Class 1 Cold Water Biota
Class 1 Warm Water Biota

Table 5-3 – Typical Water Quality Standards
Dissolved
Oxygen (mg/L)
Water Quality
8 Good
4.5-6.5 Moderately
Impaired
Temperature
The rates of biological and chemical processes depend on temperature. Aquatic organisms from microbes to fish are dependent on certain temperature ranges for their optimal health. Optimal temperatures for fish depend on the species: some survive best in colder water, whereas others prefer warmer water. Benthic macroinvertebrates are also sensitive to temperature and will move in the stream to find their optimal temperature. If temperatures are outside this optimal range for a prolonged period of time, organisms are stressed and can die. Temperature is measured in degrees Fahrenheit (F) or degrees Celsius (C).
For fish, there are two kinds of limiting temperatures the maximum temperature for short exposures and a weekly average temperature that varies according to the time of year and the life cycle stage of the fish species. Reproductive stages
(spawning and embryo development) are the most sensitive stages.
Temperature affects the oxygen content of the water (oxygen levels become lower as temperature increases); the rate of photosynthesis by aquatic plants; the metabolic rates of aquatic organisms; and the sensitivity of organisms to toxic wastes, parasites, and diseases.
Temperature Cycling
Changes in temperatures are seasonal. Because water is an excellent insulator organism in aquatic systems are isolated from temperature swings. In terrestrial systems temperature changes per a 24 hour cycle may be from 10-40 degrees.
In aquatic systems these changes do not occur.

Causes of temperature change include weather, removal of shading streambank vegetation, impoundments (a body of water confined by a barrier, such as a dam), and discharge of cooling water, urban storm water, and groundwater inflows to the stream. pH pH is a term used to indicate the alkalinity or acidity of a substance as ranked on a scale from 1.0 to 14.0. Acidity increases as the pH gets lower pH affects many chemical and biological processes in the water. For example, different organisms flourish within different ranges of pH. The largest varieties of aquatic animals prefer a range of 6.5-8.0. pH outside this range reduces the diversity in the stream because it stresses the physiological systems of most organisms and can reduce reproduction. Low pH can also allow toxic elements and compounds to become mobile and "available" for uptake by aquatic plants and animals. This can produce conditions that are toxic to aquatic life, particularly to sensitive species like rainbow trout. Changes in acidity can be caused by atmospheric deposition (acid rain), surrounding rock, and certain wastewater discharges.
The pH scale measures the logarithmic concentration of hydrogen (H+) and hydroxide (OH-) ions, which make up water (H+ + OH- = H2O). When both types of ions are in equal concentration, the pH is 7.0 or neutral. Below 7.0, the water is acidic (there are more hydrogen ions than hydroxide ions). When the pH is above 7.0, the water is alkaline, or basic (there are more hydroxide ions than hydrogen ions). Since the scale is logarithmic, a drop in the pH by 1.0 unit is equivalent to a 10-fold increase in acidity. So, a water sample with a pH of 5.0 is
10 times as acidic as one with a pH of 6.0, and pH 4.0 is 100 times as acidic as pH 6.0. pH Cycling pH cycling in aquatic systems occurs on a diel cycle and is very dependent upon the buffering capacity of that system (see alkalinity section). In well buffered systems pH changes are minimal. Without adequate buffer changes may swing into both the acidic and alkaline ranges.
In a typical stream pH is usually around 6. This is due to the organic acids leaching from leaves and other woody material into the stream. Some streams will be slightly higher and some lower depending upon the impact of woody

debris removal from the system. Thus, high pH in streams can sometimes indicate loss of organic matter input and impact from urbanization and other disturbances.
Additionally, photosynthesis has a tremendous impact upon pH. The consumption of CO
2
by plants from the water during photosynthesis has the effect of raising the pH. A pH as high as 10 in water that is poorly buffered and very eutrophic is very possible. When considering pH it is important to take into consideration these biological influences.
Conductivity
Conductivity is a measure of the ability of water to pass an electrical current.
Conductivity in water is affected by the presence of inorganic dissolved solids such as chloride, nitrate, sulfate, and phosphate anions (ions that carry a negative charge) or sodium, magnesium, calcium, iron, and aluminum cations
(ions that carry a positive charge). Organic compounds like oil, phenol, alcohol, and sugar do not conduct electrical current very well and therefore have a low conductivity when in water. Conductivity is also affected by temperature: the warmer the water, the higher the conductivity. For this reason, conductivity is reported as conductivity at 25 degrees Celsius (25 C).
Conductivity Cycling
Conductivity in streams and rivers is affected primarily by the geology of the area through which the water flows. Streams that run through areas with granite bedrock tend to have lower conductivity because granite is composed of more inert materials that do not ionize (dissolve into ionic components) when washed into the water. On the other hand, streams that run through areas with clay soils tend to have higher conductivity because of the presence of materials that ionize when washed into the water. Ground water inflows can have the same effects depending on the bedrock they flow through.
Discharges to streams can change the conductivity depending on their make-up.
A failing sewage system would raise the conductivity because of the presence of chloride, phosphate, and nitrate; an oil spill would lower the conductivity.
The Conductivity is measured in micromhos per centimeter (µmhos/cm) or microsiemens per centimeter (µs/cm). Distilled water has a conductivity in the range of 0.5 to 3 µmhos/cm. The conductivity of rivers in the United States generally ranges from 50 to 1500 µmhos/cm. Studies of inland fresh waters indicate that streams supporting good mixed fisheries have a range between 150

and 500 µhos/cm. Conductivity outside this range could indicate that the water is not suitable for certain species of fish or macroinvertebrates. Industrial waters can range as high as 10,000 µmhos/cm.
Alkalinity
Alkalinity is the ability for water to neutralize an acid. This is measured by titration with strong acid. This addition of acid provides H + to the system and the greater amount of H + the system can assimilate without pH change the greater the alkalinity. Increased concentrations of phytoplankton also increase alkalinity.
Hardness measures the concentration of calcium and magnesium ions present.
Sources of Calcium Carbonate (CaCO
3
) or Magnesium Carbonate (MgCO
3
) into the system are sedimentary rock especially calcareous (limestone) and soils with free carbonates (minerals). We consider this to be hard water. Hard igneous rock or soils leached or bound add little buffer to water. We consider this soft water with ranging pH
Alkalinity Cycling
The cycling of alkalinity is in reality tied into the CO
2
buffer system. This system is the primary buffering mechanism in freshwater and very important to understand. The Carbon Dioxide – Bicarbonate system – Carbonic Acid can be visualized as:
CO
2
+ H
2
O
Carbon dioxide
H
2
CO
3
H + + HCO
3
2H + + CO
3
2-
Carbonic Acid Bicarbonate Carbonate
Carbon dioxide is very soluble in water and acts to acidify water. When dissolved in water in equilibrium with carbonic acid and entire process.
Photosynthesis consumes CO
2
and respiration adds CO
2
to system. To compensate for the equilibrium, carbonic acid dissociates into H + and bicarbonate and bicarbonate disassociates into carbonate and H + . In eutrophic waters pH often driven as high as 10 by photosynthesis.
Oxidation-Reduction Potential (ORP)
ORP measures the availability or concentrations of electrons. An abundance of electrons creates a high ORP and the limited availability of electrons creates a low ORP. It is similar to the idea of acids and bases – lots of one or the other. In

aquatic systems chemicals have the tendency to accept or donate electrons. This ties in with DO. High DO then high ORP.
ORP Cycling
Organic decomposition and change in chemical constituents can occur in the presence of any number of terminal electron acceptors, including O
2
, NO
3
Mn 2+ , Fe 3+ , SO
4
=
,
. It occurs most rapidly in the presence of oxygen, and slower for other electron acceptors. ORP changes through the sequence of electron acceptors, as O
2
is the acceptor at 400-600 mV. Nitrate becomes an acceptor at
250 mV, manganese at 225 mV, iron between +100 and -100 mV, sulfides at -
100 to -200 mV and carbon, or CO
2
, will become the terminal electron acceptor below -200 mV.
Essentially, 500 is magic number for ORP. It represents the healthy side of oxidation where the terminal electron acceptor is oxygen. When changes occur often chemical or biological disturbance is responsible for those changes.
Carbon
Organic carbon provides the energy inputs that drive the stream ecosystem.
Autochthonous input provides organic material that a stream receives from production that occurred within the stream (i.e., primary production by periphyton, macrophytes, and phytoplankton). Allochthonous input provides organic material that a stream receives from production that occurred outside the stream channel
(i.e., plant litter).
Coarse particulate organic matter (CPOM) is the material directly falling or carried into the stream from terrestrial ecosystems. It includes leaves, needles, plant parts, woody debris (all allochthonous inputs) and macrophytes during diebacks (autochthonous generated production). CPOM is the major source of organic input in low-order woodland streams and is produced in seasonal pulses.
It is of greatest abundance during fall and winter months. It is roughly defined as particles greater than 1 mm in size.
Fine particulate organic matter (FPOM) is breakdown products from CPOM, feces from small consumers, from DOM by microbial uptake, sloughing of algae, and forest floor litter and soil. FPOM is the major of organic input in mid order streams. It is roughly defined as particles less than 1 mm and more than 0.5 um in size.

Dissolved organic matter (DOM) as particles less than 0.5 um in size. It includes allochthonous inputs from groundwater sources, surface flow, leachate from detritus of terrestrial origin, and throughfall. Autochthonous sources include extracellular release and leachate from algae and macrophytes.
Carbon Cycling
Assimilation is the uptake of carbon to create biomass. Remineralization occurs as organisms excrete nutrients. Organic carbon is generated to CO
2
through respiration. Microbes can oxidize reduced chemicals under low redox (reduced environment creating energy and oxidized chemicals release energy when reduced.
Phosphorus
Both phosphorus and nitrogen are essential nutrients for the plants and animals that make up the aquatic food web. Since phosphorus is the nutrient in short supply in most fresh waters, even a modest increase in phosphorus can, under the right conditions, set off a whole chain of undesirable events in a stream including accelerated plant growth, algae blooms, low dissolved oxygen, and the death of certain fish, invertebrates, and other aquatic animals.
There are many sources of phosphorus, both natural and human. These include soil and rocks, wastewater treatment plants, runoff from fertilized lawns and cropland, failing septic systems, runoff from animal manure storage areas, disturbed land areas, drained wetlands, water treatment, and commercial cleaning preparations.
Phosphorus has a complicated story. Pure, "elemental" phosphorus (P) is rare. In nature, phosphorus usually exists as part of a phosphate molecule (PO
4
).
Phosphorus in aquatic systems occurs as organic phosphate and inorganic phosphate. Organic phosphate consists of a phosphate molecule associated with a carbon-based molecule, as in plant or animal tissue. Phosphate that is not associated with organic material is inorganic. Inorganic phosphorus is the form required by plants. Animals can use either organic or inorganic phosphate.
Both organic and inorganic phosphorus can either be dissolved in the water or suspended (attached to particles in the water column). Orthophosphate – PO
4
-3 is the dissolved portion of phosphorus in water and readily available for uptake

by plants. It is measured directly on filtered samples – filtered to remove organic component.
By contrast total phosphorus – TP is the total component of phosphorus in water.
It measures all phosphorus in water and organisms in water. It is measured on samples after digestion with strong acid.
Of significance is the iron – phosphorus complexes that occur in natural waters.
Ferric phosphate – FePO
4
occurs under oxic conditions (high ORP) binding it to iron thus making it unavailable to plants. Under anoxic conditions it disassociates creating (Fe 2+) and PO
4
3- availability to plants. Often if this phosphorus availability is transported downstream it can create eutrophic conditions.
Phosphorus Cycling
Phosphorus cycles through the environment, changing form as it does. Aquatic plants take in dissolved inorganic phosphorus and convert it to organic phosphorus as it becomes part of their tissues. Animals get the organic phosphorus they need by eating either aquatic plants, other animals, or decomposing plant and animal material.
As plants and animals excrete wastes or die, the organic phosphorus they contain sinks to the bottom, where bacterial decomposition converts it back to inorganic phosphorus, both dissolved and attached to particles. This inorganic phosphorus gets back into the water column when animals, human activity, chemical interactions, or water currents stir up the bottom. Then plants take it up and the cycle begins again.
In a stream system, the phosphorus cycle tends to move phosphorus downstream as the current carries decomposing plant and animal tissue and dissolved phosphorus. It becomes stationary only when it is taken up by plants or is bound to particles that settle to the bottom of pools.
In the field of water quality chemistry, phosphorus is described using several terms. Some of these terms are chemistry based (referring to chemically based compounds), and others are methods-based (they describe what is measured by a particular method).
The term "orthophosphate" is a chemistry-based term that refers to the phosphate molecule all by itself. "Reactive phosphorus" is a corresponding

method-based term that describes what you are actually measuring when you perform the test for orthophosphate. Because the lab procedure isn't quite perfect, you get mostly orthophosphate but you also get a small fraction of some other forms.
More complex inorganic phosphate compounds are referred to as "condensed phosphates" or "polyphosphates." The method-based term for these forms is
"acid hydrolyzable."
Monitoring phosphorus
Monitoring phosphorus is challenging because it involves measuring very low concentrations down to 0.01 milligram per liter (mg/L) or even lower. Even such very low concentrations of phosphorus can have a dramatic impact on streams.
Less sensitive methods should be used only to identify serious problem areas.
While there are many tests for phosphorus, we will measure total phosphorus
(TP). The total phosphorus test measures all the forms of phosphorus in the sample (orthophosphate, condensed phosphate, and organic phosphate). This is accomplished by first "digesting" (heating and acidifying) the sample to convert all the other forms to orthophosphate. Then the orthophosphate is measured by the ascorbic acid method. Because the sample is not filtered, the procedure measures both dissolved and suspended orthophosphate.
Nitrogen
Nitrates are a form of nitrogen, which is found in several different forms in terrestrial and aquatic ecosystems. These forms of nitrogen include ammonia
(NH
3
), nitrates (NO
3
), and nitrites (NO
2
). Nitrates are essential plant nutrients, but in excess amounts they can cause significant water quality problems. Together with phosphorus, nitrates in excess amounts can accelerate eutrophication, causing dramatic increases in aquatic plant growth and changes in the types of plants and animals that live in the stream. This, in turn, affects dissolved oxygen, temperature, and other indicators. Excess nitrates can cause hypoxia (low levels of dissolved oxygen) and can become toxic to warm-blooded animals at higher concentrations (10 mg/L) or higher) under certain conditions. The natural level of ammonia or nitrate in surface water is typically low (less than 1 mg/L); in the effluent of wastewater treatment plants, it can range up to 30 mg/L.

Sources of nitrates include wastewater treatment plants, runoff from fertilized lawns and cropland, failing on-site septic systems, runoff from animal manure storage areas, and industrial discharges that contain corrosion inhibitors.
Nitrogen gas (N
2
) is most abundant form of nitrogen. It is difficult for plants to use because bond is very strong and hard to break. Plants use ions instead.
Nitrogen occurs in several ionic forms each with a specific importance to freshwater and derived through specific bacterial mediations. Ammonia (NH
3
) or free ammonia is the reduced form of nitrogen. It is in balance with ammonium
(NH
4
+ ) in freshwater. Ammonium is released at high pH and is very toxic to fish creating burning across gills.
Nitrite (NO
2-
) is the partially oxidized form of nitrogen or the intermediate step through oxidation to nitrate. Nitrite is toxic to plants and animals. Nitrate (NO
3is the oxidized form of nitrogen. It is readily taken up by plants and readily
) available.
Total inorganic nitrogen (TIN) is Ammonia + Nitrate + Nitrite + Ammonium. Total
Keldajal Nitrogen (TKN) is the total nitrogen component. It measures all nitrogen in water – available in water and component in biota. It requires digestion with strong acid for measurement.
Nitrogen Cycling
Nitrates from land sources end up in rivers and streams more quickly than other nutrients like phosphorus. This is because they dissolve in water more readily than phosphates, which have an attraction for soil particles. As a result, nitrates serve as a better indicator of the possibility of a source of sewage or manure pollution during dry weather.
Water that is polluted with nitrogen-rich organic matter might show low nitrates.
Decomposition of the organic matter lowers the dissolved oxygen level, which in turn slows the rate at which ammonia is oxidized to nitrite (NO
2
) and then to nitrate (NO
3
). Under such circumstances, it might be necessary to also monitor for nitrites or ammonia, which are considerably more toxic to aquatic life than nitrate.
Nitrogen Fixation – N
2
gas to ammonia (NH
3
).
N
2
+ 3H
2
2NH
3

This is accomplished by specialized bacteria in the root nodules of legumes
(soybeans, alfalfa and clover). Heterocysts in water by blue-green algae and bacteria.
Nitrification - Ammonia is then through a two-step process converted to nitrite
(NO
2
) and then to Nitrate (NO
3
). Ammonification – Nitrogen in plants and animals is converted back to ammonia (NH
3
) and ammonium (NH
4
) by decomposers.
Denitrification – specialized bacteria (Often found in wetlands) convert ammonia
(NH
3
), nitrate (NO
2
) and nitrate (NO
3
) back into atmospheric nitrogen gas (N
2
and
N
2
O).
Sulfur
Sulfur is present and available depending upon ORP. Sulfate - SO
4
is the oxidized form of sulfur in water. It is utilized by specialized bacteria in water.
Hydrogen sulfide (H
2
S) (rotten egg smell) is the reduced form of sulfur.
Sulfur Cycling
H
2
S) reduced to sulfur (S) by bacteria in soil and water. Sulfur then returns to
SO
4
through reactions completing the cycle.
Nutrient Limitation and Spiraling in Lotic Systems
Nutrient limitation occurs when a key nutrient typically phosphorus or nitrogen limits the growth of producers. All plants require nutrients to grow and the
Redfield ratio is 16:1 for Nitrogen to phosphorus as optimal. Watersheds continually supply lotic systems with ample supplies of nutrients. The role of limitation in lotic systems is complex – short-term enhancement of producers through fertilization is transferred to consumer population through longer-term experimentation
Phosphorus is generally the limiting nutrient in the environment because it is in such short supply. In eutrophic systems, nitrogen becomes limiting because phosphorus is so abundant. Nutrients throughout the summer months are tightly bound in biota creating very limited availability for new growth of plant material.

Nutrient Spiraling
Biota only has short-time hold on nutrients due to one way flow. Thus plants hold on to nutrients until they die and are released. Spiral length is related to:the transport of nutrient in water (typically the largest component). Uptake and transport by biota (low spatial but great temporal impact). Spiral length related to rate of flow and composition of biota.

Chapter 6 - Biological Characteristics of Streams
Background
Aquatic biology is used in conjunction with water chemistry to provide a good estimation of stream water quality. These measures take some expertise to obtain and in some instances are difficult to quantify between streams and over time. The advantages to this approach are that organisms are integrators of their environment and not the snap shot water chemistry provides. By measuring biological indicators we get a sense of the stresses that occur over time. These organisms cannot escape pollution. While chemical analysis is limited to the direct measurements taken at the time of sampling, biological measures describe conditions in the stream over long periods of time. Indices and patterns have been developed to compare stream water quality.
Periphyton
Source of energy to lotic food webs. Groups of autotrophs (macroalgae – visible to the naked eye) in periphyton are:
 Chrysophyta – Golden Brown Algae– Diatoms
 Chlorophyta – Green Algae
 Chyanophyta – Blue-green Algae
Periphyton is attached to substrate. Periphyton attached to stones are epilithon.
They form dense growth on surfaces and are firmly attached. When attached to sediments it is epipelon. Typically forms a mat on surface and is easily swept away through currents. When attached directly to other plants it is considered epiphyton. The growth on plant surface can be detrimental to host plant in dense growths and it is firmly attached.
The community structure of periphyton communities occurs in layers Adpressed describes periphyton in close contact with substrate. Pedunculate occurs with attachment only at base producing erect growth form. Longitudinal community shifts (upstream, downstream) with the species-assemblage zonation along the river continuum. Temporal (seasonal) community shifts with peak abundance and diversity typically occurring in late summer or early fall. Spatial patchiness among microhabitats is common. Diatoms are the predominant group found in river periphyton.

High flows may scour and sweep away periphyton . Current influences substrate types which influences periphyton substrate availability. Current brings a constant flow of nutrients from upstream (nutrient spiraling concept). Algae are light limited, and may be sparse in heavily shaded streams. Early spring, before leaf out, may be a better sampling index period in shaded streams.
Algae have short generation times (one to several days), they respond rapidly to environmental changes. Samples of the algal community are "snapshots" in time, and do not integrate environmental effects over entire seasons or years.
Pheriphyton As Water Quality Indicators
1. These algae are primary producers and the foundation of stream food webs. This makes them excellent indicator species.
2. These organisms also stabilize substrata and serve as habitat for many other organisms. Because benthic algal assemblages are attached to substrate, their characteristics are affected by physical, chemical, and biological disturbances that occur in the stream reach during the time in which the assemblage developed.
3. Diatoms in particular are useful ecological indicators because they are found in abundance in most lotic ecosystems
4. Diatom species are differentially adapted to a wide range of ecological conditions
5. Blue greens occur in abundance at high enrichment rates and chlorophytes at medium rates
Freshwater Macroinvertebrates
The animals living in a stream provide the best indicators of that stream’s overall health and ecological condition. Human activities that alter a watershed and interfere with the natural processes of a stream have immediate as well as longlasting effects on the animals that live in the stream. We monitor invertebrates because they represent an enormous diversity of body shapes, survival strategies, and adaptations. Many invertebrates require clear, cool water, adequate oxygen, stable flows, and a steady source of food in order to complete their life cycles. Below are descriptions of the invertebrates you might expect to find at an excellent stream site (i.e., a site unchanged by humans), a moderate site, and a poor (i.e., degraded) site.

Macroinvertebrates life history describes the growth and life cycle. Each moves from egg – juvenile instars – pupation – adult. The frequency these organisms compete this transition on an annual cycle is called voltinism – frequency with which the life cycle is completed within a year. Occurrences of voltanism in macroinvertebrates are as follows:
 Univoltine
 Bivoltine
 Multivoltine
 Semivoltine
 Merovoltine
Temperature triggers pupation to adult. As adults there are many differing strategies for reproduction. In some species such as mayflies it is fast. Eggs are laid soon after mating. In stoneflies it is slow. Adults feed before depositing eggs on substrate. Mating location is available. Some mate in the air while others on certain substrate. Seasonal cycles are variable as well. Some that are slow may not reach adult stage until a year with the larvae growing very slowly. Others have very fast growing larvae where several cycles may be exhibited by the same species within a year.
Figure 6-1. Caddisflies

Habitat selection by mated female for deposition of eggs occurs through a series of cues. Many cues and behavior patterns such as temperature and chemical cues lead females to spot for eggs deposition. Various species have extended flight, oviposition or hatching periods to deal with varying environmental conditions.
Fecundity is highly variable between species. Numbers of eggs varies from 100
– 10000 depending on species. This may often be a function of female size and development. Eggs are sometimes reabsorbed if conditions unfavorable.
Insects are able to lay eggs immediately after pupation. Often the hatching time period of eggs may be extended to minimize risks. Growing larvae may move through ontogenetic niche shifts or remain in the same niche. Those with very limited niche are specialists. These orgainisms speicialize on particular prey but are more efficient digesters of food. Generalists have a very broad niche and greater survivorship when conditions are harsh. They have the ability to collect when shredding food depleted.
Table 6-1 – Functional Feeding groups of Macroinvertebrates
Shredders CPOM – plants, leaves, wood
Plecoptera,
Ephemeroptera,
Coleoptera, Diptera,
Tricoptera decomposing matter
– Ephemeroptera,
Hemiptera,
Coleoptera, Diptera,
Tricoptera
Scrapers Periphyton Ephemeroptera,
Hemiptera,
Coleoptera, Diptera,
Tricoptera
Ephemeroptera,
Coleoptera, Diptera,
Tricoptera,
Hemiptera

During each stage of growth the organisms molt. This is a shedding of the thick exoskeleton allowing for the growth in size. For most aquatic insects a majority of the life cycle is spent in the water. Metamorphosis occurs when the larvae transpose into the adult stage. During metamorphosis the insect is very vulnerable to predation. Until the wings are fully developed the insect has no defense. Several stratigies have evolved to deal with this problem. Some emerge at night to minimize predation. Others display mass emergence to overwhelms predators overwhelm predators.
Macroinvertebrate Groups
Here are generalized descriptions of each major macroinvertebrate group
Mayflies (Ephemeroptera)
Larvae
1. Elongate bodies slightly flattened
2. Wing pads present on thorax
3. Three pairs of segmented legs from thorax
4. Gills on some segments preceding last segment
5. Gills attached to sides of abdomen – some over top and bottom
6. Gills as flat plates of filaments
7. Three long and thin tails, a few with two
Life History
1. Uni, Multi and semi voltine
2. Eggs deposited on water surface or dropped from air
3. Eggs hatch week to several months
4. 3-6 months as larvae
5. 12-27 molts
6. Emergence a. Float to surface and emerge from skin as a raft – very quick b. Emerge from pool or quite area – slower c. Subimago – not full adult and must molt again into imago. Unique to mayflies. Subimago with hairs on wings giving dull appearance
7. Adults do not feed and have no mouthparts – die soon after mating often within 24 hours

Stoneflies (Plecoptera)
Larvae
1. Elongate bodies slightly flattened
2. Long-thin antennae project from head
3. Wing pads on thorax but may only be visible on older larvae
4. Three pairs of segmented legs from thorax
5. Two claws at the end of segmented legs
6. Gills on bottom of thorax or no gills
7. Gills as single or branched filaments
8. Two long thin tails project from abdomen
Life history
1. Uni, semi and mero voltine
2. Emerge in all months of the year – unique to insects
3. Eggs laid in water as a mass – break apart and fix to bottom
4. Eggs hatch in 3-4 weeks
5. 10-11 months as larvae
6. molt 10-22 times
7. Must crawl out of water to molt into adult – 5-10 min for final molt
8. Adults live 1-4 weeks
9. Adults feed on plant material – rarely fly only to new habitat or to disperse eggs
10. Attract mate through drumming – crawl to each other
11. Winter stones only active in cold months
Caddisflies (Trichoptera)
Larvae
1. Head with thick hardened skin
2. Antennae short and usually not visible
3. No wing pads on thorax
4. Top of thorax with hardened plate – in some two and three hardened
5. Three pairs of segmented legs from thorax
6. Single and branched gills on abdomen – some with no gills
7. Pair of prolegs and claw on end of abdomen
8. Portable cases and retreats
Life History
1. Bi, uni and semi voltine
2. most emerge from late spring to early fall
3. eggs laid in a gelatinous mass or bare in water – maybe a bright color
4. females will walk underwater laying eggs

5. Some similar to megaloptera – larvae fall into water
6. larval stage 2-3 months or as long as 2 years
7. molt 5 times maybe 6 or 7
8. silk glands in lower lip – use silk to make homes and retreats
9. homes used for camouflage, physical protection, food acquisition and respiratory efficiency – oxygen diffuses across body and they wriggle in tube to help facilitate this
10. all make cocoon to pupate – allowing water to circulate
11. pupa stage – 2-3 weeks
12. float to surface and emerge as adults
13. fly to vegetation live for 30 days
14. Adults stay in leaves – eat only liquid food – nectar
15. Mate with males in swarms
Dragon and Damselflies (Odonata)
Larvae
1. Lower lip (labium) long and folded against head
2. Wing pads on thorax
3. Three pairs of segmented legs from thorax
4. Two claws on legs
5. No gills on abdomen – some gills on end of abdomen
Life history
1. Univoltine
2. Most deposit eggs on water – some in plants
3. hatch in one to several weeks
4. ten months as larvae range of 5-6weeks to 5-6 years
5. molt 10-12 times
6. Must climb out of water for final stage of emergence – do not feed
7. 1-3 hours of emergence – predation concerns
8. Adults live 1-2 months and do not reproduce right away
9. Excellent vision and predators in flight – eat mosquitoes, other dragonflies and butterflies
10. Defend territories – wing damage
11. Stay with female after mating – may help female underwater to lay eggs
True Flies (Diptera)
Larvae
1. Head capsule like or reduced to look continuous with thorax or further reduces to just mouthparts from thorax
2. no wing pads on thorax

3. No segmented legs
4. Pro-legs may be present
5. Thorax and abdomen composed of entirely soft skin or possibility of hardened plates
Life History
1. all types
2. emerge during warm weather – spring through fall
3. eggs laid in water in all kinds of configurations – on objects and free floating
4. hatch in several days to 2 weeks
5. larvae as several weeks to several years
6. molt 3-4 times
7. winter as larvae
8. most pupate in same place as larval development
9. some molt in skin – some make a cocoon
10. float to surface and emerge – raft
11. adults as several days to 2 weeks
12. most live on fluids – stay near aquatic habitat except those that feed on blood
13. mate through swarming, posts, objects and your head serve as swarming areas
True Bugs (Hemiptera)
Larvae
1. Mouthparts as a beak or short cone
2. Wing-pads on thorax
3. Three pairs of legs from thorax
4. Two claws on end of some legs
5. No gills
Life History
1. Bi and multi voltine
2. Adults may hibernate in winter not dia-pause
3. Eggs attached to objects underwater or just above surface
4. eggs hatch 1-2 weeks
5. 2 months as larvae
6. molt 4-5 times
7. do not leave water for final molt as they breath air
8. adults in fall and mate in spring – live 6 mos as adults
9. Hide in mud during hibernation

Water Beetles (Coleoptera)
Larvae
1. Head with thick hardened skin
2. Thorax and abdomen with thick hardened skin – underside soft
3. No wing pads on thorax
4. Three pairs of segmented legs from thorax – some no legs
5. No structures from sides in most – some with flat plates or stout filaments
6. No prolegs or filament at end of abdomen
Life history
1. Uni voltine
2. Over-winter as adults
3. Females lay eggs below water surface on solid object
4. Eggs laid in the spring – hatch 1-2 weeks
5. Larval development in 6-8 summer months
6. molt 3-8 times
7. Final molt in soil – dig cell to pupate may be in plants or other objects
8. 4-6 weeks in cell – molt, skin hardens
9. Emerge as adults but do not mate until spring. Live as adults 1 year
Other Flies (Megaloptera)
Larvae
1. Head and thorax with thick hardened skin – abdomen soft
2. Prominent chewing mouthparts in front of head
3. No wing pads
4. Three pairs of segmented legs from thorax
5. Seven or eight pairs of stout tapering filaments stick out from sides of abdomen
6. End of abdomen has prolegs with two claws or single long tapering filament with no claws.
Life History
1. Semi, uni and mero voltine
2. Adults emerge in late spring to summer
3. Eggs deposited out of water on hanging objects such as longs and leaves in a mass at night
4. Eggs hatch in 1-2 weeks at night
5. Young drop in water below the egg mass – have gas bubbles to help them float to suitable location
6. 1-3 years as larvae

7. molt 10-12 times
8. Larvae leave water for final molt – often together helgramite crawling
9. build cell in soil and stay 1-14 days to pupate
10. Adult crawls out of cell. Lives 3 days for male and 8-10 for female
11. Adults do not eat – fly only to find mate
12. Jaws of adult used in mating to attach to female
Use in Water Quality Characterization
Excellent stream site
Here we find a variety of organisms with high biodiversity (or taxa richness) indicating a site with low human influence: most of the animals on this guide sheet should be present in a riffle sample. Several different types (or taxa) of stoneflies, mayflies, and caddisflies indicate a healthy site. More than one type of riffle beetle may also be identifiable, some are longer and skinnier than others. Some caddisflies are tolerant of degradation, so a large number of caddisflies does not necessarily indicate a good site, especially if they are the same species.
Moderate stream site
The total number of different types of organisms (taxa richness) declines as degradation increases. About half to two-thirds the number of taxa found at an excellent site are found in a moderate site. The primary change from an excellent site is that there will be many fewer taxa of stoneflies. Mayflies will be present, but probably fewer taxa as well. Several types of caddisflies may be present depending on the type of degradation. The relative proportions of softbodied worms, baetid mayflies, simuliid flies, or amphipods may increase.
Beetles are probably still present; molluscs are not.
Poor stream site
The total number of taxa will be low. Most of the taxa found are soft-bodied animals, e.g., fly larvae, oligochaetes, nematodes, and in very poor sites, leeches and planaria. Worms are often difficult to distinguish from each other because their shapes are similarly adapted to living in soft sediments. Stoneflies are absent entirely. The only mayflies present are probably baetids (a family of mayflies). Caddisflies may be present, but only a few tolerant types. Amphipods are often present. There may be a large proportion of a single type of animal. In general, animals present may be smaller than those found at an excellent site.

Metrics of Water Quality
Family Biotic Index (FBI)
The Family Biotic Index is an index developed on the sensitivities of specific macroinvertebrates. Species or familes of macroinvertebrates are assigned a value from 0 (extremely sensitive) to 10 (very tolerant) of organic pollution. The biotic index is calculated by multiplying the tolerance value for each species by the number of individuals summing these products then dividing by the total number of individuals. A value is calculated determining the water quality of the sampled stream. Water quality values based on FBI appear below:
Table 6-2 Water quality comparisons for FBI Index
Family Biotic Index Water Quality
0.00-3.75
3.76-4.25
4.26-5.00
Excellent
Very Good
Good
Degree of Organic
Pollution
Organic Pollution Unlikely
Possible Slight Organic
Pollution
Some Organic Pollution
Probable
5.01-5.75 Fair
5.76-6.5 Fairly Poor
Pollution Likely
Substantial Pollution
Likely
6.51-7.25 Poor Substantial Pollution
Likely
7.26-10 Very Poor Severe Organic Pollution
To calculate FBI you must multiply the FBI number by the number of species.
FBI numbers can be found in Hilsenhoff or other publications. Multiply the number of individuals by its tolerance value. Total all of these products. Divide the total of tolerance value/individuals products by the total number of individuals in the sample. This is the biotic index value.
EPT Index (Based on the Numbers of EPT Species in samples)
EPT describes the number of Families of Ephemeroptera (mayflies), Plecoptera
(stoneflies) and Trichoptera (Caddisflies) found in an a sample. Each is an

indicator of pollution and generally accepted as clean-water specimens (Lenat
1988). Expected ranges are >10 excellent water quality, 6-10 slightly impacted,
2-5 moderately impacted and 0-1 severely impacted.
>10
6-9
2-5
Excellent – Non Impacted
Good – Slight Impact
Fair – Moderate Impacts
0-1 Poor – Severe Impact
To determine EPT add the total number of EPT families found in the samples.
This is your EPT number.
Percent Model Affinity (PMA) (Adherence to theoretical model of un-impacted abundance)
PMA is a measure of similarity to a non-impacted or target stream community based on percent abundance in 7 major groups (Novak and Bode 1992). An ideal community based on Washington (1984) with a community based on 40%
Ephemeroptera, 5% Plecoptera, 10% Trichoptera, 10% Coleoptera, 20%
Chironomidae, 5% Oligochaeta and 10% other. Levels of impact are descried as
>64 non impacted, 50-64 slightly impacted, 35-49 moderate impact and <35 severely impacted. Water quality based on PMA appears in Table 4.
Indicated water quality based upon Percent Model Affinity
Model Affinity
>64
50-64
35-49
Water Quality
Excellent – Non Impacted
Good – Slight Impact
Fair – Moderate Impacts
<35 Poor – Severe Impact
To calculate PMA first determine the percent contribution for each of the 7 major groups: Oligochaeta, Ephemeroptera, Plecoptera, Coleoptera, Trichoptera,
Chironomidae, and other. These must add up to 100.
For each group find the absolute difference in percentage from the model value for that group. Add up the differences.
Multiply the total of differences by 0.5 and subtract this number from 100. This is your PMA

Example:
Difference
Coleoptera 9 10 1
Other 2 10 8
Total 100 100 78
Total absolute difference = 78
78 X 0.5 = 39
100 – 39 = 61 – PMA value
Freshwater Fishes
Background
The collection of fishes adds additional information for us in the study of water quality. Similar to macroinvertebrates, fish are integrators of their environment.
Changes in fish assemblages reflect potential changes in water quality. Fish occupy a higher level on the food chain thus reflecting greater levels of complexity and potentially greater impact from pollution. Fish are very mobile and thus integrate greater stretches of stream giving us a larger picture of potential impact. As with all other measures the study of fish provides us with additional information on the condition of the streams we are studying.
Seasonality
When we study fish populations temperature is important. Generally warmer waters allow for a greater collection of fish as activity is heightened and fish are active. Some concerns exist during reproductive periods in the spring and fall.
Generally, the preferred sampling season is when stream and river flows are moderate during the spring through late summer and fall. In our sampling we

must be sensitive to flow and turbidity. We will not sample directly after storm events as the rivers are too high and too turbid to see the fish.
Fish Characteristics
Fish are characterized by various features. The location of the mouth relative to the head is very useful in identifying fish and determinations of niche. When the mouth is located front and top of head it is considered superior in attachment.
The extreme front is terminal and under the head is inferior. The gills contain an arch of bone where gill filaments are attached. These filaments are where gas exchange occurs. Two arteries run through the gills. The afferent take deoxygenated blood from heart to gills and the efferent take oxygenated blood from gills to body. The gills are protected by bony structures called gill rakers.
These also serve as sieves to collect food particles from the water. In particle feeders these gill rakes are well developed and the teeth are not. In fish predators the gill rakers are not as well developed and the teeth are. Finally, the operculum occurs at the juncture of the head and the body and the opercular flap extends over the gills for protection.
Body shape may be flattened, compressed or cylindrical. Each shape impacts swimming and correlates well with the niche of the fish. Scales cover the and provide protection. Mucus covers the scales providing the fish protection from microbial infections. Various scale types occur:
 Placoid – sharks – do not increase in size as fish grows – just adds more scales. Rectangular base
 Cosmoid – two basal layers of bones – similar to placoid and oval in shape - lungfish
 Ganoid – rhomboid in shape with interlocking peg and socket joints – paddlefish and gars
 Ctenoid – rough posterior margin – scales grow with fish – overlapping scales
 Cycloid – smooth margin – scales grow with fish and overlap.
Lateral lines provide the sensory system in fish. It is a system of ducts and openings. Free nerve endings at opening of each duct provide stimuli to the brain. Fish are very sensitive to water pressure and thus compression waves.
The lateral lines allow fish to move in synchrony with its environment.

The fins act as stabilizers for the fish. The dorsal fin runs along the top of the fish and may be of one or two parts. The first is usually spinous and provides defense from predators. The second is soft. The caudal fin is the tail and can give clues as to speed and agility of the fish. The anal fin runs along the anus.
The pectoral fins protrude perpendicular from the body attached behind the operculum and the pelvic fins are attached to the bottom. Each fin has a specific purpose in feeding, swimming and stabilization.
Fish may contain other structures as well. Barbles are sensory organs used to find food and aid in navigation. Catfish commonly have these wisker type structures attached off the corners of the mouth. Another common structure is tubercles. These are used to combat other males, stimulate and guide females and dig holes. Blue head chub is covered with tubercles to assist in building of nests from stones.
Figure 6-2. Darters

Common Fish Functional Groups
Clupeidae
Description – silvery, flat sided fishes. Sharp edged scales on the belly. Large eye covered by transparent membrane. Most marine with some freshwater.
Examples - Shad
Cyprinidae
Description – Largest family of fishes – very diverse. One dorsal fin, abdominal pelvic fins, cycloid scales and lateral line. Lack teeth in the mouth but do have teeth deep in the throat to grind food. Strictly freshwater.
Examples – Chub, Shiner, Dace, Minnow, Stoneroller
Catostomidae
Description – Mouth located on underside of head (terminal), paired fins attached low on body, fins supported only by rays (no spines), lips thick and fleshy with surface folded and possibly papillae. One dorsal fin and caudal fin is forked.
Examples - Jumprocks, Suckers, Redhorse
Ictaluridae
Description – nocturnal and often omnivorous. Lack of scales, sharp spines in pectoral and dorsal fins and fleshy fin on back between dorsal and caudal fin.
Small eyes and barbells near mouth that aid in navigation, taste and touch.
Large mouth with bristle like teeth. A mild venom in spines.
Examples – Madtom, Bullhead
Salmonidae
Description – Elongate body, adipose fin, single dorsal fin, paired fins low on the body and lack of spines. Small cycloid scales loosely embedded in the skin.
Teeth on the jaws. Small auxiliary process – projection located at base of pelvic fin.
Example- Trout
Moronidae
Description – compressed and moderate or deep body. Ctenoid scales, thoracic pelvic fins and complete lateral lines. Dorsal fins separated. First dorsal fins with nine spines, second with one spine and 11-14 rays. Three spines in anal fin.
Example - White and Striped Bass

Centrarchidae
Description – moderate deep to very deep body. First and second dorsal fin joined. Similar to Moronidae – three spines on anal fins.
Examples – Sunfish, Crappie, Bass
Percidae
Description – Two dorsal fins separate or weakly joined. One or two spines in anal fins. Pelvic fins with one spine and five soft rays located in the breast area.
Examples – Darters, Walleye
The Index of Biological Integrity
The Index of Biotic Integrity (IBI) is an index used to describe the individual condition or biological health of a stream. Dr. James Karr first developed it for use in small warmwater streams. Since that point is has been modified for use throughout the United States and elsewhere.
We will use a modified version of the IBI to reflect the condition of waters in
Virginia. We will use the nine measurements described below. The measure is scored with a 5 if it reflects a system with very little human influence and a 1 if it departs significantly from a reference stream. A score of 3 is given to a sight with intermediate qualities. Therefore when sampling the streams a perfect score is
45 and a minimal score is 9. We will use this data in conjunction with other measures to develop water quality indicators for the streams.
Measurement 1 – Total number of fish species. This measurement decreases with increased overall degradation. The number of fish species is also affected by stream size so consistency of stream order when comparing streams is important with this measurement. Reductions in total number of fish species reflect degradation from many sources of human influence (i.e. sedimentation, urbanization, toxics) so this should be used only as a general measure. In
Virginia it is typical to find 2-10 species in small creeks, 15-30 species in middlessized streams and 20-40 species in rivers. By percentage you typically find minnows 32-44%, percids 16-29%, sunfishes 9-21%, suckers 7-16% and catfishes 2-9%.
Measurement 2 – Total number of darter species/Relative percent of darter species to the total. This measure decreases with increasing sedimentation and decreased benthic oxygen supply. The many darter species found in our area are benthic insectivores living in riffles and feeding primarily on mayflies, stoneflies and caddisflies found in these riffle communities. As sedimentation

degrades riffle habitat, darter species begin to disappear. This measure may be used as an indicator of both sedimentation and toxic substances.
Measurement 3 – Total number/relative percent of water column insectivores.
This number generally decreases with the loss of riparian vegetation. This number will increase with channelization and conversion of riffle habitat. In this area sunfish species good representatives of water column insectivores.
Measurement 4 – Total number/relative percent of pool-benthic insectivores.
This is a measure of sedimentation and channelization as pool-benthic habitat increases. In this area the proportion of bluehead chub and white suckers are good measures.
Measurement 5 – Total number/relative percent of intolerant species. This measure distinguishes high and moderate quality sites using species that are intolerant of various chemical and physical perturbations. Intolerant species are typically the first species to disappear following a disturbance. Species are dependent on local conditions.
Measurement 6 – Relative abundance of tolerant species. This measurement increases with human influences. It is a general measure of degradation.
Proportions of green sunfish, white sucker and creek chubs are good indicators here.
Measurement 7 – Relative abundance of omnivores or generalist feeders. The percent of omnivores in the community increases as the physical and chemical habitat deteriorates. As the invertebrate food source decreases in abundance and diversity due to habitat degradation (e.g., anthropogenic stressors), there is a shift from insectivorous to omnivorous fish species. Omnivores consistently feed on substantial quantities of plant and animal material.
Measurement 8 – Relative abundance of top carnivores. This measure discriminates between systems with high and moderate integrity. Systems with high integrity are able to support adequate (up to 10%) populations of sport fish piscivores. In our systems small mouth bass are a good measure of top carnivores. Sampling gear is sensitive to this measure.
Measurement 9 – Deviation from ideal or number of individuals in sample. This measure is expressed as catch per unit effort, either by area, distance, or time sampled. It may also be expressed as the deviation from an ideal community as measured throughout the region. Generally sites with lower integrity support

fewer individuals. Abundance is not always the best measure of pollution impact and deviation from ideal provides a better measure.
To calculate the IBI each of the above measures is evaluated on a scale of 0-5.
If observed measures meet all the criterion described in each measurement the measure is scored a 5. Thus the greatest IBI score allowable on these measures is a 45. If the score is not a 5 the evaluator begins to determine if the criterion are somewhat in agreement or not in agreement at all. If none of the measures are in agreement the measurement is scored a 0 and if some are present it is scored 1-4 depending upon the level of agreement. While this type of scoring is qualitative it does provide a good measure of water quality in a stream based upon fish metrics.

Chapter 7 – Ecological Characteristics of Streams
Habitat
It is important to understand how the organisms of study in streams interact with their environment. Many times we have questions of scale such as how many organisms might inhabit a stream reach. Here we are asking questions of population size describing the number of individuals in a population at a given time. We may also have interest in population density describing the number of individuals in a certain space at a given time. These are questions of scale and must be understood and quantified.
Issues also revolve around the dispersion of populations. Many patterns exist:
Random - position independent of others - rare.
Regular - position evenly distributed at frequency greater than chance - rare.
Aggregated - position clustered around a common resource or refuge . May have regular or random distribution within aggregations - must consider scale.
Fine grain - individuals surrounded by other species relative to its own
Course grained - individuals surrounded by its own species relative to others
High intensity - wide variation in density of patches
Low intensity - little variation in density of patches
Organisms tend to cluster around resources and this often explains these patterns we see. Additionally, when resources become limiting organisms will disperse. In streams this may be passive in the case of drift. Drift occurs when the organisms release hold of their current position and flow downstream to a random new location. In this way the organism is hedging its bets that better resources exist downstream. Recolinization of organisms upstream occurs when winged adults mated and deposit eggs.
Active dispersion occurs when the organism has control over where the organism goes.
This may be a result of predictable stream flow or wind dispersion in adults. All these events are driven by stochastic or deterministic events. Stochastic events are unpredictable. Changes in rainfall or weather is a stochastic event. Drift may be purely stochastic in that the organisms drift for unspecified times and distances. A deterministic event is the leaf fall during fall months supplying the stream with nutrients and food throughout the course of the year. Cranefly life cycle is much in tune with this event as the larvae hatch to eat leaves in synchrony with the event.
Deterministic inputs to streams:
Nutrients
Sedimentation
Urbanization
Fertilization

Stochastic inputs to streams
Genetic – changes in populations through drift
Demographic – changes in populations due to random differences among individuals
Environmental – changes in populations due to unpredictable responses to weather, disease, competition
Catastrophes – events occurring at random that cause a large proportion of population disturbance
Ecosystem Ecology and Stable Steady States
Perturbations can occur as natural events or through human activity. Natural events such as floods create opportunity for recolonization and succession of organisms. It releases nutrients and creates new opportunities for uptake elsewhere in the stream.
Human activity in the form of agriculture or urbanization releases excesses in nutrients, toxics and sedimentation. These excesses are difficult for the stream to metabolize and results in eutrophication.
Typically it is phosphorus that is of concern with eutrophication. These is very little phosphorus in the water in relation to need and of the phosphorus in the environment most if not all of it is tied into biomass of organisms. Human activity upsets this balance in many ways. Artificial fertilizers made from oil contain high concentrations of phosphorus. From agriculture to household application much of the excess runs over land and into water courses. Detergents contain phosphorus as a cleaning agent and the excess delivered to the waste water treatment plants enters the streams. But by far the greatest contributor if erosion as sediment contains tremendous quantities of phosphorus. When released it become soluble into water and leads to eutrophication.
Impacts to aquatic systems are many fold. Increases in primary producers occurs when plants increase growth based upon the excess phosphorus. Periphyton can overwhelm grazers in streams leading to the loss of EPT. Blue green algae growth increase many fold. As this excessive plant growth decays bacteria consume oxygen leading to fish kills. Excessive bacteria can grow leading to diseases in predatory fishes. Often lose top predatory fish and they are replaced by omnivores. The entire system is out of balance.
Ecological Stability and Sustainability
The ability of an aquatic system to deal with these changes in inputs relates to its stability. Stability describes the positive and negative feedback loops required to maintain constant dynamic change in response to changing environmental conditions.
Consider the following ecological concepts:
Persistence – ability to resist change
Constancy – ability to maintain
Resilience – ability to rebound after a disturbance

Each aquatic system is able to internalize and metabolize stream inputs in variable ways. A large river or lake may be very persistent but not resilient. A small stream is very resilient but not persistent. And then there is the issue of diversity. What level of diversity will promote stability? Typically a more diverse system is stable. Yet often disturbance creates greater diversity and is this a stable system? This leads to the idea of alternative stable steady states.
Alternative Stable Steady States
“Clean”   State   “Polluted”   State
Polluted   or   Disturbance
Figure 7-1 – Model of alternative steady states
Systems can remain without impact from inputs of pollution for periods of time. It is then that only a small disturbance can create a large impact to these systems. As depicted in figure 7-1, these systems can be envisioned as a pushing a marble up an incline as the system is disturbed. The system resists this as it is difficult to push the marble up hill. As the perturbation continues the marble eventually reaches the summit and it takes very little energy to push the system into a polluted state. In many instances we see this pattern in nature.

Conditions of alternative stable steady states of existence i. Initial inputs of disturbance leave ecosystem relatively undisturbed
– marble is resistant to change as if pushing it up hill ii. Continued disturbance forces change but ecosystem is resistant – must continue disturbance to push uphill iii. At a point change occurs and ecosystem moves into new state very rapidly and with very little disturbance iv. Remains in new state and must be pushed uphill again to return to pre disturbed condition. v. Changes from oligotrophic to eutrophic
In order to protect and preserves aquatic systems conservation and management programs are being established. Far too often we simply react to an issue trying to fix only the symptoms and not the problem. By establishing long term monitoring programs and watershed management plans a much better framework of proactive management can be established.

Stormwater
Stormwater or non-point source pollution is one of the greatest threats to stream health.
This is water flowing over land, storm drains, and worst of all impervious surfaces.
Rainfall or snowmelt moving over land surfaces is responsible for this flow and deposits pollutants into lakes and rivers often during very large storm events.
Stormwater pollutants are many fold. It contains excess fertilizers, herbicides, and insecticides from agricultural lands and residential areas. There are oil, grease, and toxic chemicals from urban runoff and energy production. Sediment from improperly managed construction sites, crop and forest lands, and eroding stream banks. Salt from irrigation practices and acid drainage from abandoned mines. Bacteria and nutrients from livestock, pet wastes, and faulty septic systems. Atmospheric deposition from hundreds of miles away and heavy metals from sewage systems.
The impacts of stormwater on freshwater are numerous. Porous landscapes like forests, grasslands and wetlands trap stormwater and allow it to slowly filter into ground.
Through this filtration stormwater is stored, treated and then slowly returned to streams all year. Nonporous landscapes like parking lots, buildings, allow water to accumulate and directly run into water bodies in large discharge events. The water is released directly into water course without any treatment. To avoid flooding, stormwater is channelized and unloaded full force into streams creating stream erosion problems.
This destroys streamside vegetation, widens stream channels, results in lower water depths during non-storm periods and higher water depths during storm periods. Water moving downstream has increased sediment loads and higher water temperatures.
Macroinvertebrates and other aquatic life are scoured from the stream bottom.
Eventually the increased sediment and pollution load reaches lakes and estuaries creating eutrophication and long lasting effects on the lake ecosystems.
Stormwater Regulation
Total Maximum Daily Load (TMDL) is the current methodology used by the
Environmental Protection Agency to protect receiving water systems from stormwater pollution. A TMDL calculates the maximum amount of a pollutant that a water body can receive and still meet water quality standards. Once that calculation is made an allocation of that amount to the pollutant's sources occurs allowing only enough pollutant into a stream that will maintain identified use.
This process helps identify use of water body, develop regulations mandate that states, territories, and authorized tribes list impaired and threatened waters and develop
TMDLs. For non point source control of pollutants the best treatment is the use of Best
Management Practices (BMPs). These BMPs provide control of stormwater before release into a stream.

Here is a list of possible BMP measures in streams.
 Infiltration
 Bioretention
 Wetlands
 Wet Pond
 Pavement
Figure 8-1 – Check Dams from a Sedimentation Pond

Figure 8-2 – Stormwater Retention Pond
These measures are functional and successful to a limited extent. Often in the sourtheastern United States much of the sediment is clay. Basins and structures do not provide adequate retention time for clay particles to settle out of water. As a result, lighter clay particulates continue out of the BMP structures and into streams and water courses. There is an effort to regulate more clay using things such as polymers to coagulate clay into the size particulate that the BMP structures can remove.
Water Quality Improvement Through Stream Restoration
Stream restoration is an effort to return the stream to an effective size and shape to handle water loads being forced upon them. As is typical in urban settings the erosion causes the stream banks to become vertical and incised. This results in channelized water flowing through the stream. Stream restoration may involve simple inexpensive solutions to complex expensive ones. The ideal solution is to stabilize stream banks to prevent further erosion and rework eroded ones to return functionality to them.

Possible BMPs from streams include:
 Fencing – keeps livestock out of streams. Livestock tend to accelerate erosion going in and along the stream bank.
 Shaped Slopes – by reshaping the slopes from incised or undercut to a more natural slope this minimizes erosion.
 Urban Plantings – plant roots will stabilize and strengthen bank slopes.
 Watershed Management Plans – by coordinating planning efforts with localities the development that creates erosion and stream impacts will be minimized.
 In stream Improvements – any effort to create habitat, remove large debris fallen into the stream through erosion and maximize stream flow is beneficial.
 Hydraulic Structures – efforts such as the use of root wads and rip rap can minimize the impact from high flow events.

Chapter 9 – Data Analysis and Experimentation
Simple Experimental Design
Observations
This is where you want to make some simple observations about the environment that you would like to study. You need to know what physical conditions are in the area, what the biotic and abiotic factors are, and what organisms are present. Scientists must first familiarize themselves with the environment that they wish to study.
Research
A little research about an area helps scientists understand what is already known about their potential research area. This can be done using the library or by talking to other people who are familiar with the area. Research can help answer some basic questions and focus your experimental question.
Hypothesis
Once we have a question we want to make some predictions about what we expect to happen. Here we will form an If ….then…. because statement. It should read: If I do this or change this, then the organism’s response will be this, because of the impact of the environment.
Methods and Materials
This is where you spend most of your time planning out the research. There are several things that must be taken into consideration in this section.
 Variables – this is what you want to change in your experiment. Your variables are what you want to alter in order to answer your research question. If you want to know hoe temperature affects organism than your variable in the temperature.
 Treatments – the treatments are the different conditions that you will create in order to test your variables. You want to create a standard environment and then each treatment changes the one variable you are trying to test.
 Controls – every experiment needs to have controls. These are the things that you do not change. These are the constants that you make sure stay

the same so that any differences between your treatments can be attributed to your variables.
 Replicates – for each treatment that you have to test your hypothesis you want to have several replicates in order to get an average answer. The goal is not to find out what could happen in extremes but what is most likely to happen in the different treatments.
 Data collection – this is important to think about before hand. What data do you want to collect and record in order to test your hypothesis? You also need to consider how to measure your results. Will you need a ruler, a stopwatch, a scale?
 Materials needed – once you have a plan you want to create a materials list that will include all the equipment needed in order to carry out the experiment.
Results
Most results are recorded in a table of some form so that recording and later reading the results is easy. What is important in a results section is turning the data collected into a form that can be easy viewed and discussed. This usually involved making graphs of some sort, and computing averages. Bar graphs, line graphs and pictograms are all useful in displaying results.
Discussion
One of the most important parts of the discussion is to re-address the hypothesis statement. Either you gained evidence to support you hypothesis or not.
Experiments do not prove ideas, they gain evidence for theories. A theory is only proved or becomes a scientific law when tried and tested by many people over many years. You also want to address an experimental errors that may have occurred due to equipment or human errors. State what the errors were and how you would correct them the next time. Discussions should also include what you would improve on for next time and what other questions came up during the procedure. Many experiments may collect evidence for one question but many more come up during the process.
The discussion also needs to include some sort of explanation and discussion of the results. You need to explain and answer the question "So What?" Why are the results you found relevant and interesting? How does this relate to the

organism and the environment in which it lives? Answering so what? can be difficult but it is this discussion that can be the most interesting in research. This discussion often also leads to many new questions and research ideas to further explore ideas.
Outline of Data Analysis a. Objectives of Study – What do we want to know when we are done? i. Biological Questions ii. Chemical Questions iii. Ecological Questions iv. Management Questions b. Sampling and Monitoring Plan i. What variables to study ii. What techniques to use iii. When will we collect samples iv. Where will we sample v. How many replicates per visit vi. How long vii. How will assessment be analyzed

c. Data Management i. Analyzed for trends and conclusions ii. Produced and stored in a form easily accessed and analyzed iii. Quality Control d. Presentation of Results i. Technical and detailed analysis ii. General Analysis