U.S. Geological Survey
Texas Water Science Center
A Proposal Submitted to the North East Texas Municipal Water District
Modified Biological Assessment Procedures for the Evaluation of
Aquatic Biota in Relation to Environmental Flow Prescriptions in
the Cypress Basin of Northeast Texas
By J. Bruce Moring
U.S. Department of the Interior
U.S. Geological Survey
Cypress Bayou
draft 18 Jun 2007
Pg 1 of 10
30 April 2009
Introduction
The United States Army Corp of Engineers (USACE), The Nature Conservancy (TNC), Caddo
Lake Institute (CLI), Northeast Texas Municipal Water District (NETMWD), United States
Geological Survey’s Texas Water Science Center (USGS-TWSC), and many local stakeholders
jointly held a Cypress Basin Environmental Flows Workshop in Jefferson, Texas on December
2nd – 4th, 2008. The principal objectives of the workshop were for the USGS-TWSC and CLI to
summarize their efforts to evaluate the accuracy of selected environmental flow prescriptions for
Big Cypress Creek, and to reach consensus among the agencies and stakeholders regarding the
proposed revisions to the selected flow prescriptions for Big Cypress Creek, acceptance of
existing flow prescriptions for Black Cypress Bayou and Little Cypress Creek, and determine
future environmental flows research and monitoring in the Cypress Basin. The proposed
revisions to selected flow prescriptions for Big Cypress Creek, and the existing flow
prescriptions for Black Cypress Bayou and Little Cypress Creek were accepted at the December
2008 meeting in Jefferson. Those in attendance agreed that the approach taken to evaluate the
accuracy of flow prescriptions for Big Cypress Creek was transferable to Black Cypress Bayou
and Little Cypress Creek.
The Cypress Basin Environmental Flows Technical Committee held a meeting in Austin on
January 13th, 2009 to discuss future environmental flows research and monitoring in the Cypress
Basin. Committee members agreed on the need for an approach to monitor the status of aquatic
biota in relation to selected environmental flow prescriptions for Big Cypress Creek, Black
Cypress Bayou, and Little Cypress Creek. Committee members also agreed to evaluate the
potential to augment existing bioassessment procedures used by NETMWD in the Cypress Basin
to include methods to evaluate aquatic biota in relation to selected environmental flow
prescriptions. Staff with NETMWD and USGS-TWSC agreed to collaborate to develop and
implement modified bioassessment procedures to evaluate the relation of low-flow
environmental flow prescriptions to the status of aquatic biota at three sites --- one each on Big
Cypress Creek, Black Cypress Bayou, and Little Cypress Creek (fig. 1).
Cypress Bayou
draft 18 Jun 2007
Pg 2 of 10
Bio-assessment site
Figure 1. Major sub-basins of the Cypress Basin and approximate location of proposed
environmental flows bioassessment sites.
Objectives
1. Design an approach specific for Cypress Basin streams that augments existing
bioassessment procedures used by NETMWD CRP program with Texas IFP-approved
bioassessment procedures for fish and benthic macroinvertebrates.
2. Complete modified bioassessments of Cypress Basin sites within the range of low-flow
environmental flow prescriptions for each stream within the critical index period
mandated by CRP.
3. Analyze the relationship of environmental flow prescriptions to mesohabitat-specific
composition, abundance, and distribution of fish and benthic macroinvertebrates at
selected sites in the Cypress Basin.
Cypress Bayou
draft 18 Jun 2007
Pg 3 of 10
Relevance and Benefits
The USGS-TWSC is submitting this proposal to support continued efforts between the USACE,
USGS-TWSC, CLI, NETMWD, and TNC in the evaluation, refinement, implementation, and
monitoring of environmental flow prescriptions for the Cypress Basin including the major
tributaries to Caddo Lake; Big Cypress Creek, Black Cypress Bayou, and Little Cypress Creek.
The Cypress Basin is home to wetlands of international significance as recognized by the Ramsar
Convention of 1971 (Ramsar, 2008), several threatened aquatic and terrestrial species (Texas
Parks and Wildlife Department, 2008), a Texas State Park, and a U.S. Fish and Wildlife Service
refuge. The State of Texas Instream Flows Program (TIFP) has taken a particular interest in the
Cypress Basin environmental flows effort because it represents the first basin-wide stakeholder
driven environmental flows project in Texas similar to the basin-wide projects the IFP began in
2007-08 under Texas Senate Bill 3.
This proposed study is a unique opportunity for the TWSC and NETMWD to collaborate with
the Texas IFP and the Texas Commission on Environmental Quality’s (TCEQ) Clean Rivers
Program (CRP) to complement existing stream bioassessment procedures (currently required of
Clean Rivers Program partners such as NETMWD) with procedures designed to monitor biotic
status and response to environmental flow prescriptions. Together, NETMWD and other CRP
partners operate the most extensive network of stream bioassessment sites in Texas. Selected
sites in this state-wide network could be used to implement modified bioassessment procedures
to evaluate and monitor for biotic response to environmental flow prescriptions as these
prescriptions are translated into flow recommendations or flow standards for the various priority
rivers basins under review as mandated by Texas Senate Bill 3.
Approach
Design of an Augmented Bio-assessment Approach
The USGS TWSC in cooperation NETMWD, TCEQ CRP, and Texas IFP will design an
approach that compliments existing TCEQ CRP bioassessment procedures with accepted Texas
IFP assessment procedures (TWDB, 2008) for fish and benthic macroinvertebrates. The
modified approach will ensure that NETMWD CRP obtains the required bioassessment data and
related metrics required by TCEQ CRP while also acquiring data and information in support of
the long-term monitoring of biota in relation to selected environmental flow prescriptions for Big
Cypress Creek, Black Cypress Bayou, and Little Cypress Creek.
The USGS TWSC and NETMWD will develop a detailed study work plan that will be available
for review by the technical leads for the Texas IFP from the Texas Water Development Board,
Texas Parks and Wildlife Department, and the TCEQ. A meeting hosted by USGS-TWSC and
NETMWD will follow the technical review and approval of the work plan, and a presentation of
the study design will be provided to all interested parties at a Caddo Basin Watershed Protection
Cypress Bayou
draft 18 Jun 2007
Pg 4 of 10
Plan Meeting or at the annual Clean Rivers Program Steering Committee Meeting for the
Cypress Basin.
Reach Establishment and Mesohabitat Delineation
An assessment reach will be established on Big Cypress Creek, Black Cypress Bayou, and Little
Cypress Creek consistent with TCEQ Source Water Quality Assessment (SWQM) protocols
(TCEQ 2007), and will be 40 times wetted channel width determined during low-flow
conditions, and not greater than 0.6 miles or one full meander of the channel. The reach will be
collocated with USGS study sites where hydrologic connectivity of in-channel features has been
completed in Big Cypress Creek, and will be done later this year in Black Cypress Bayou and
Little Cypress Creek as part of a separate project. Reach establishment at USGS study sites is
critical because water levels already obtained from continuous monitors, and associated stream
discharge can be related to the number, distribution, and area of delineated mesohabitats and the
biota collected in these habitats.
The number, distribution, and area of mesohabitats (e.g., riffles, runs, glides, pools, and
backwater) will be determined for each reach at a flow that is within the range of average to dry
year low-flow prescriptions that were adopted at the December 2008 Cypress Basin Flows
Workshop in Jefferson, Texas (Caddo Lake Institute, 2008) for each stream. These flows will be
suitable for biological sampling according to TCEQ SWQM protocols (TCEQ 2007). The lowflow prescription range for average to dry years for the July to September critical period is 40 to
6 cfs for Big Cypress Creek, 4 to 32 cfs for Black Cypress Bayou, and 5 to 26 cfs for Little
Cypress Creek. Mesohabitat assessment will be done concurrently with fish and macrobenthic
invertebrate sampling under the same flow conditions, and generally on the day prior to
biological sampling to allow the reach to “rest” prior to biological sampling. Mesohabiat
delineation and biological sampling will be done for two consecutive years in the three reaches.
The outline for each mesohabitat (e.g., rapid, riffle, run, pool, glide, backwater) will be drawn in
the field on a pen-tablet PC as geo-referenced polygons using ArcMAP®. Each mesohabitat will
be mapped, and physical measures of velocity, depth, bed substrate, and cover will be collected
at five representative points in each mesohabitat (Parasiewicz, 2007). The number and total area
of stable woody snags in each mesohabitat will be recorded to support the calculation of a
mesohabitat structure index (Moring, 1999). Mesohabitat mapping will be done by loading the
PC with a two-dimensional map of the channel margin and thalweg that will be completed for
each site after a reach has been selected. The two-dimensional map will be loaded into ArcMap®
on the PC, and will serve as a template for mesohabitat mapping. Each mesohabitat will be fieldmapped using the touch screen on the notebook computer, and the area of each masohabitat will
be determined within the range of targeted low-flow prescriptions. A detailed map of each reach
will be produced and will include the sequence, type, and area of each mesohabitat.
Cypress Bayou
draft 18 Jun 2007
Pg 5 of 10
Fish
A fish community survey will be completed at each site following the TCEQ Source Water
Quality Monitoring Protocol (TCEQ 2007) augmented by methods as detailed in Texas IFP
protocols (TWDB 2008). Boundaries of the mesohabitats that were mapped prior to fish
sampling will be marked, and fish will collected, identified, enumerated, and vouchered from
each mesohabitat. Each mesohabitat will be electrofished using boat, barge or backpack
equipment depending on current and depth, sampled until no additional species are collected and
the entire habitat has been sampled. Electrofishing will be repeated for each mesohabiat and the
time electrofished in each mesohabitat recorded with a total minimum total of 900 seconds for
the reach. At least 10 seine hauls, distributed equally among mesohabitat types, will be done
after electrofishing is completed. Block-netting between mesohabitat to minimize fish movement
will be used as needed. Seined fish will be identified, enumerated, and vouchered by
mesohabitat. External anomalies such as fin erosion, lesions, and body condition will be
recorded. Fish not identified in the field will be preserved, labeled by mesohabitat, and returned
to the USGS TWSC for preliminary identification with subsequent verification or identification
by ichthyologists with the University of Texas Natural Science Center in Austin, Texas.
The number of species and the total and relative abundance of each species by mesohabitat will
be determined. Each fish will be classified by reproductive, habitat, and trophic guild. Reachbased metrics will be determined for the calculation of a regional fish Index of Biotic Integrity
(IBI) as per TCEQ SWQM protocols.
Benthic Macroinvertebrates
A snag and supplemental traveling-kick benthic macroinvertebrate sample will be collected in a
representative mesohabitat such as a riffle, run or glide in each reach consistent with TCEQ
SWQM protocols (TCEQ 2007). The samples collected from the preferred mesohabitat type will
not be combined, but will be inspected for the number of organisms to ensure minimum sample
size, and preserved separately for each mesohabitat sampled. The mesohabitats not sampled
initially will be sampled by collecting a snag and supplemental traveling-kick sample in each
one. Each mesohabitat sample will be preserved on site with 70 percent denatured alcohol. Each
sample will be submitted to a contract laboratory for identification and enumeration of benthic
invertebrate taxa to the lowest taxon possible. Each sample will be processed in the laboratory
using a 300-count sub-sampling routine to ensure an adequate sample size of benthic organisms
from each mesohabitat sample.
Taxa richness, total (i.e., estimated from sub-sampling) and relative abundance, and a suite of
metrics and tolerance and trophic classifications will be determined for the organisms in each
mesohabitat sample. The reach-based benthic macroinvertebrate data and metrics required by
TCEQ SWQM will be obtained using a computer-generated 175 ± 20 percent-count randomized
sub-sampling routine from the combined targeted mesohabitat sample data.
Cypress Bayou
draft 18 Jun 2007
Pg 6 of 10
Freshwater mussels will be sampled in each mesohabitat using a quadrat sampling procedure
(Wisconsin Department of Transportation, 2005). The number of quadrats per mesohabitat will
be determined by the size of the mesohabitat with at least one quadrat sampled in each
mesohabiat. The species, total and relative abundance, and the number of mussels per unit area
will be recorded for each mesohabitat. Depth, near-bed velocity, dominant substrate, mussel size,
and bed compactness will be recorded for each mussel or mussel bed if the mussels are too close
together to record these measurements for each individual organism.
Data Analysis
Data analysis will emphasize the evaluation and selection of biological indicators that are
mesohabitat rather than reach-specific, and are thought to be most responsive to shifts away from
the natural flow regime as defined in this study by the low-flow environmental flow prescriptions
for these Cypress Basin streams. Guild structure and taxa richness of fishes and benthic
macroinvertebrates in each mesohabitat will be evaluated, and mesohabitat-specific abundance
and distribution of threatened species such as the Bluehead shiner and critically imperiled
mussels such as the Louisiana pigtoe and Sandbank pocketbook will be noted. Freshwater
mussels will be sampled using a quadrat-based procedure that will allow detailed quantitative
comparison of mussel species richness, abundance, and microhabitat distribution between
mesohabitats.
The mapping of mesohabitats will provide an opportunity to compare differences in mesohabiat
sequence, area, physical, and biological characteristics between what will most likely be two
different flows within the low-flow range of flow prescriptions during the two summers of data
collection. The USGS-TWSC and NETMWD could decide to intentionally target a high and low
flow within the range of low-flow prescriptions for each assessment reach, and this option will
be discussed during the development of a more detailed project work plan.
Products
1. Development of bioassessment procedure that augments existing TCEQ CRP methods
with methods to evaluate the status of aquatic biota in relation to selected environmental
flow prescriptions.
2. Detailed reach maps including delineated mesohabitats, reach structure, and map insets
indicating the type and area of each mesohabitat.
3. Fish and benthic macroinvertebrate data (including freshwater mussels) and metrics by
mesohabitat and reach in a format as requested by NETMWD and TCEQ.
4. A U.S. Geological Survey Scientific Investigation Report comparing within and between
reach taxonomic and physical habitat data and metrics over the range of flow
prescriptions observed during sampling.
Cypress Bayou
draft 18 Jun 2007
Pg 7 of 10
Timeline
Field mapping and biological sampling of mesohabitats in a representative reach in Big Cypress
Creek, Black Cypress Bayou, and Little Cypress Creek will take place in the mid to late summer
of the first two years of the study during the appropriate index period as defined by TCEQ
SWQM. Benthic invertebrate samples will be submitted for ID and enumeration, and all
biological and physical mesohabitat data and metrics will be determined and compiled at the end
of each year of sampling. Data analysis and report preparation will take place during the third
year of the study, and all products will be provided to NETMWD on or before September 30,
2012.
Task
Fy 2010
Fy2011
Oct-Nov-Dec-Jan-Feb-Mar-Apr-May-Jne-Jly-Aug-Sept
Oct-Nov-Dec-Jan-Feb-Mar-Apr-May-Jne-Jly-Aug-Sept
Work plan
preparation and
project planning
Mesohabitat mapping
and biological
sample collection at
three sites in the
Cypress Basin
Submittal of benthic
invertebrate samples
to contract laboratory
for analysis.
Date entry, metric
calculation, and
general data
management and
review
Data analysis
Report writing and
preparation
Cypress Bayou
draft 18 Jun 2007
Pg 8 of 10
Fy2012
Oct-Nov-Dec-Jan-Feb-Mar-Apr-May-Jne-Jly-Aug-Sept
Personnel
Biologists, hydrologists, and hydrologic technicians with the Investigations Section of the Texas
Water Science Center in Austin, Texas, will be involved in the project. The principal personnel
to be involved and their responsibilities are listed in the table below.
Title
Responsibility
Bruce Moring
Jeff Mabe
John Rosendale
Erin Sewell
John Gordon
Principal Investigator and Lead Biologist
Assistant Biologist
Hydrologic Technician
Hydrologic Technician
Hydrologist (Publications Specialist)
Budget Table
Budget Year
Budget Category
FY 2010
FY 2011
FY 2012
Labor
Equipment and Supplies
Contract Laboratory (benthic
invertebrates)
Publications
Vehicles
Travel
$ 55,565
$ 4,960
$ 5,800
$ 55,514
$ 3,866
$ 6,380
$ 55,360
$ 2,816
$ 2,320
$ 6,264
$ 2,350
$ 6,890
$ 13,920
$
500
$ 2,404
USGS Cooperative Match
NETMWD
$ 25,000
$ 50,000
$ 25,000
$ 50,000
$ 25,000
$ 50,000
Total Budget
$ 75,000
$ 75,000
$ 75,000
Cypress Bayou
draft 18 Jun 2007
Pg 9 of 10
References
Caddo Lake Institute, 2008, December 2008 Flows Workshop,
http://www.caddolakeinstitute.us/decflowsmeeting08.html
Harwell, M.A., Myers, V., Young, T., Bartuska, A., and Gassman, N., 1999, A framework
for an ecosystem integrity report card: BioScience, v. 49, p. 543–556.
Moring, J.B., 2003, Baseline assessment of fish communities, benthic macroinvertebrate
communities, and stream habitat and land use, Big Thicket National Preserve, Texas, 1999–
2001: U.S. Geological Survey Water-Resources Investigations Report 03–4270, 33 p.Moring,
Parasiewicz, P., 2007, The mesohabsim model revisited: River Research Applications, v. 23, p.
893-903.
RAMSAR List, 2008, The List of Wetlands of International Importance
(http://www.ramsar.org), 42 p.
Texas Commission on Environmental Quality, 2007, Surface Water Quality Monitoring
Procedures, Volume 2: Methods for Collecting and Analyzing Biological Assemblage and
Habitat Data, RG-416, 202 p.
Texas Parks and Wildlife Department, 2008, Endangered and Threatened Species,
http://www.tpwd.state.tx.us/huntwild/wild/species/endang/
Texas Water Development Board, 2008, Texas Instream Flows Progran: A Technical Overview,
Report 369, 148 pages.
Wisconsin Department of Transportation, 2005, Guidelines for sampling freshwater mussels in
wadable streams, Wisconsin Department of Transportation Research, Development, and
Technology Transfer, Report No. 0092-01-09, 50 pp.
Cypress Bayou
draft 18 Jun 2007
Pg 10 of 10