Introduction/Background The Middle Rio Grande Basin Valley extends from Cochiti Lake downstream to San Acacia. It covers approximately 3,060 square miles in central New Mexico. The counties within that area are Santa Fe, Sandoval, Bernalillo, Valencia, Socorro, Torrance, and Cibola (USGS, 2012). Cochiti Dam Cochiti Dam was completed November 1973 to provide flood control and sediment retention. Cochiti Dam controls a drainage area of about 37,800 km2 (Richard & Julien, 2003). Construction of the dam has resulted in significant impacts downstream including degradation of the channel bed and coarsening of the bed from sand to gravel size (Richard & Julien, 2003). Decreased spring peak flows and the incision of the bed of the Rio Grande following construction of Cochiti Dam has resulted in a river channel that is detached from its floodplain. Cottonwood forests are now competing with exotic species such as Russian Olive, Siberian Elm, and Asian Saltcedar or tamarisk. Restoration Beginning in 1996, the Santa Ana Pueblo initiated a restoration project that has resulted in restoration of 115 acres of native grassland and 235 acres of cottonwood bosque through removal of exotic species. The project has also lowered the floodplain by one meter in some of the 10 km of river within the pueblo (Richard & Julien, 2003). Restoration effort have been aimed at removal and eradication of non-native vegetation, lowering of the floodplain to allow inundation at high flows, and widening of the channel to increase biodiversity of in-channel habitat (Richard & Julien, 2003). IV. Restoration Project Bosque Del Apache Over the centuries the Rio Grande had developed a rich riparian corridor inhabited by diverse species including migrating birds and tall trees. The major factor for the rich ecosystem was the river’s periodic flood pulse that allowed water to stretch across the floodplain and subsidize the earth and biological organisms. Today the floodplains are abandoned as the riparian corridor does not receive its historical quantities of water mainly due to dams, irrigation structures and levees. In conjunction, competition has ascended as non-native species have claimed the riparian zone and its resources over the years. Due to the consequences of degradation efforts have been mobilized to rehabilitate the river and its riparian zone. SaltCedar Control One such attempt is taking place at the Bosque del Apache National Wildlife Refuge near Socorro, NM. The efforts there concentrate on reconnecting the floodplains to the river, restoring riparian habitats, and reducing the non-native saltcedar population. Firstly, a saltcedar control that has been practiced for over 50 years is active uprooting implanted by heavy machinery such as bulldozers and tractors. This method was standardized by the U.S. Bureau of Reclamation and involves cutting the root crown 30-45 cm below the surface in warm weather and dry soil (McDaniel, 1998). The scattered cuts are then piled and burned to prevent spreading of buds. Another means to control saltcedar population is the burning of piled uprooted cuttings as scattered pieces if left alone allow for buds to migrate and sprout (Bosque del Apache NWR). Herbicides, aerial and spot treatments, were practiced until the early nineties until stacked burning was implemented. Along with piled burnings control measures include smoothing the entire area of saltcedar removal by dragging a rail iron over the surface (McDaniel 1998). Concentration on saltcedar regulation involves either mechanical or chemical techniques but it is suggested that further studies regarding herbicide effects on other organisms (Springer, 1999). Experimental Seasonal Flooding In a wider perspective, flooding was experimented with over a several year study to identify the possible prospects of riparian restoration. This ecological measure of reconnecting the floodplain to the river implies many variables and species including mammals, insects, fungi, and soil bacteria.(Table 1). The study obtained baseline data over 2 years and established four study sites; two control areas with no experimental flood inundation and two sites with experimental seasonal flooding with discharge from a “nearby irrigation canal that carried a mixture of water diverted directly from the Rio Grande, irrigation return flows, and groundwater drainage accumulated in the nearby Rio Grande Low Flow Channel” (Molles, 1998). The results of the study indicate that periodic flooding produced increased abundance of soil bacteria, fungi, and cellulose decomposers. The root lengths colonized by mycorrhizal fungi and inoculum potential as well as dehydrogenase activity, soil biological activity, were greater at the flood site than the controlled (Molles, 1998). Another increase is the breakdown of leaves and release of nutrients for plant growth optimally during the early summer period. The hydraulics of the flood events allowed for woody debris and litter to be transported out of the system (Ellis et al, 1999). The biomass of woody debris was lower in the experimental site than the control, carrying out potential fuel for fires; but woody debris base data was non-existent leaving no temporal comparison. This restorative effort was a research project yet proved indicative of the potentials of seasonal flooding. The Bosque del Apache’s experimental flooding was over the course of three years and shows that over a long period of time and proven practices more indications of ecological responses from the riparian zone could be positive. At this time, because of the combination of experimental flooding, saltcedar control, and continued stewardship the Bosque del Apache Wildlife Refuge serves as a location for migrating birds and recreation. Fish Communities of the Rio Grande In most arid rivers of North America the fish assemblages have been affected by anthropogenic disturbances such as loss of habitat, water development and the introduction of non-native species (Bestgen and Platania 1991). The native fish fauna of the Rio Grande is in decline and the modern fauna include many introduced taxa (Platania 1991). The native fish community of Rio Grande within New Mexico is thought to consist of 16-27 species (Platania 1991). With the Albuquerque basin (Sandoval, Bernalillo, Valencia, and Soccoro counties, NM) (Hoagstrom et al. 2010) identified 22 native fish species and 22 species that are either non-native to their study area or non-native to the entire Rio Grande drainage. Fluvial fishes of the Albuquerque and Belen valleys are thought to have been extirpated in two periods (Hoagstrom et al. 2010). The first extirpation period, pre-1915, when Elephant Butte Dam was finalized, resulted in the disappearance of large-bodied, big-river natives (shovelnose sturgeon Scaphirhynchus platorynchus, longnose gar Lepisosteus osseus, American eel Anguilla rostrata, blue sucker Cycleptus elongatus, smallmouth buffalo Ictiobus bubalus, gray red- horse Moxostoma congestum, blue catfish Ictalurus furcatus, flathead catfish Pylodictis olivaris, fresh- water drum Aplodinotus grunniens). The historical presences of catadromous American eels within the Albuquerque valley indicate a continuous migration to the gulf of Mexico (Koster, 1957). The second extripation period, post-1915, resulted in disappearance of native fluvial minnows (Rio Grande speckled chub Macrhybop- sis aestivalis, Rio Grande shiner Notropis jemezanus, phantom shiner Notropis orca, Rio Grande blunt- nose shiner Notropis simus) that persisted long enough to be documented by historical surveys of the mid-20th century (Hoagstrom et al. 2010). The first extirpation was due to the increasing aridity and dewatering. The second extirpation of fluvial minnows (cyprinidae) has been thought to be caused by additional dams, river manipulation, urbanization, increased water withdrawals, and invasion of non-native aquatic organisms (Bestgen and Platania 1991). Rio Grande Silvery Minnow The Rio Grande silvery minnow (Hybognathus amarus) is the only remaining member of the reproductive guild of cyprinids that spawn eggs that are naturally buoyant (U.S. Fish and Wildlife Service 2010). The species was found in the Rio Grande from Espanola, New Mexico to the gulf of Mexico (Bestgen and Platania 1991), the Pecos River from Santa Rosa to the confluence with the Rio Grande (Pfieger 1980), and in the lower Jemez River and This species was once the most widespread and abundant species in the Rio Grande basin of New Mexico, Texas and Mexico (Bestgen and Platania 1991). Currently, Rio Grande silvery minnow occupies seven percent of its former range, and is fragmented by diversion dams (U.S. Fish and Wildlife Service 2010). A non-essential experimental population was reintroduced into the Big Bend reach of the Rio Grande in Texas to establish an additional self-sustaining population of H. amarus (U.S. Fish and Wildlife Service 2010). H. amarus was declared an endangered species under the Endangered Species Act in 1994. Critical habitat was designated by the Service in 2003, to include the Rio Grande downstream of Cochiti reservoir to north of Elephant Butte reservoir (252 kilometers). The lateral extent of critical habitat is defined by area that is bound by existing levees, or 91.4 meters of riparian zone adjacent to each side of the bank full stage of the middle Rio Grande (U.S. Fish and Wildlife Service 2010). Specific water management and restoration actions are required to meet the Biological Opinion written by the Service in 2003. Requirements include: Salvage of the species during river intermittency, reintroduction, interagency coordination of daily river and reservoir operations, improvements to irrigation metering and management, indirect use of native Rio Grande water, release of stored San Juan-Chama Project water, and pumping from the Low Flow Conveyance Channel to the river. The Recovery Plan (U.S. Fish and Wildlife Service 2010) also requires a strategic program to assist agencies when determining where to initiate habitat construction essential to preventing population decline or extinction. Habitat modifications should occur within occupied reaches and reintroduction areas and create flooded surfaces during the spawning period of H. amarus (U.S. Fish and Wildlife Service 2010). Hydrological and fish monitoring occurs at multiple restored and unrestored sites under similar environmental conditions to determine the effectiveness of restoration activities of H. amarus populations dynamics. The Flood Pulse in the Middle Rio Grande The flood pulse is the key driving force for the existence, productivity and interactions of the major biota in river-floodplain systems (Junk et al. 1989). Flood pulses in natural systems are regulated by a spectrum of geomorphological and hydrological conditions that can vary from unpredictable to predictable and can be relatively short lived or long term (Junk et al. 1989). Disconnection of the river and their floodplain is predominant stressor in modified rivers due to dams, flood control, interbasin diversions, and irrigation. This ecological alteration can have effect nutrient dynamics, organic matter, and the metabolism of a river from floodplain inputs (Valett et al. 2005). In arid regions, including the southwestern U.S. floods are the major ecological drivers for riparian forests, floodplains and lotic systems. In the Middle Rio Grande in New Mexico flow regulation and depletions have negatively impacted the ecological system. Valett et al. (2005) conducted a study to determine variation in ecosystem function between a connected and disconnected floodplain within the Bosque del Apache National Wildlife Refuge. Groundwater monitoring wells and surface water samples were collected to measure temperature, dissolved oxygen, dissolved organic matter, phosphate, nitrate and ammonium, total suspended solids. Floodplain metabolism was also calculated by measuring forest floor respiration CO2. Based on their findings, the group proposed that the inter-flood intervals influence the structure of floodplain by connectivity with main channel and floodplain aquifer (Valett et al. 2005). The results of this study identify the opportunity to increase flooding either naturally or manipulated to help restore the ecosystem processes within the floodplain of the Middle Rio Grande. Physical and Chemical Water Quality Urbanization alters the hydrology, water chemistry and quality, channel geomorphology, organic matter, fish and aquatic invertebrate assemblages, algae and ecosystem processes (Paul and Meyer 2001, Meyer et al. 2005, Walsh et al. 2005). Agriculture is also a major contributor of non pointsource pollution to surface waters (Moore et al. 2005, Bernot et al. 2006). Bestgen and Platania (1991) suggested that the poor water quality in the Rio Grande near Albuquerque, may affect Rio Grande silvery minnow (Hybognathus amarus) populations and overall reduced fish communities within the reach, especially during low flow periods. The U.S. Fish and Wildlife Service (USFWS) has identified water quality degradation caused by agriculture and urbanization in the Rio Grande as a factors that contribute to the decline of Rio Grande silvery minnow (Hybognathus amarus) (U.S. Fish and Wildlife Service 2010). Several studies have been undertaken in the past to assess water quality impacts in the MRG, focusing on chemical analyses and toxicity studies (metals, hydrocarbons, pesticides, PCBs, pharmaceuticals, and other constituents of potential concern) and fish health. The existing chemical and physical water quality data for the MRG and related information is extensive, and determining exact deleterious compounds or synergistic impacts is difficult. Marcus et al.(2010) completed an ecological risk assessment to assess 1) the growth, survival, and reproduction of H. amarus and 2) the general health of the aquatic community in the Middle Rio Grande (MRG). Their ecological risk assessment focused on chemical data collected by USFWS (15,624 analytical results) and the Upper Rio Grande Water Operations Study (250,000 plus analytical results). This ecological risk assessment used conservative species specific benchmarks to determine if exposure effected H. amarus and the aquatic community. Marcus et al. (2010) found to be no consistently high-risk patterns for individual potential constituents of concern (PCOCs) in the MRG. Many PCOCs are thought to be naturally occurring, and elevated due to natural sources. The results of this risk assessment do not support the conclusion that PCOCs are primary factors that contribute to the decline of the H. amarus. The physical water quality of the Middle Rio Grande has been degraded due to land use change and urbanization. DO levels have long been taken as indicators of the health of a water body (Keefer et al. 1979). DO in lotic systems is usually high, uptake from the atmosphere is high and the diurnal variation is high (coupled to photosynthesis, respiration, and decomposition) (Wetzel 2001). Dissolved oxygen sags from stormwater point discharges (Van Horn 2009; DBS&A 2009) and fish kills (Abeyta and Lusk 2004, Buhl 2004) due to DO sags have been documented in the MRG. Sediment conveyed during large stormwater events can increase turbidity and bed disturbance can limit the photic zone and aquatic plants (in Paul and Meyer 2001). It is estimated that 1.5x106 kilograms (kg) per year (3.4x106 pounds per year) of sediment and other solids are discharged into the Rio Grande (U.S. Fish and Wildlife Service 2011). Temperature change has been observed in urban streams (Paul and Meyer 2001). Native fishes in the southwest have evolved to tolerate dynamic temperature regimes (Matthews et al. 2000). Despite this adaptation, temperature has identified as potential stressor to H. amarus. Basic physical parameters of water quality (temperature, oxygen saturation, pH, salinity, total suspended sediment, and turbidity) may be more indicative of environmental conditions important to the RGSM. Currently, physical water quality parameters such as temperature, dissolved oxygen (DO), pH and salinity are evaluated in the field as part of a number of separate studies and activities, including salvage operations, population monitoring, and habitat effectiveness monitoring. Thus, the water quality data synthesis should be focused on physical water quality parameters such as temperature, dissolved oxygen, suspended sediments. Specific time periods of concern identified by USFWS (2010) are during low flows and stormwater discharge events. A large percentage of the flow consists of municipal and agricultural discharge (U.S. Fish and Wildlife Service 2010). The evaluation of past water quality data during these periods would be useful to identify if any of these parameters are limiting factors to the RGSM population in the MRG, and to help direct how we can best manage the silvery minnow population in the MRG. Understanding and analyzing the water quality parameters in the MRG, and how they relate to the health and survival of the RGSM, will improve water management schemes and habitat restoration goals that are supportive of various RGSM life stages. Conclusion Changes in the water and sediment regime of the Rio Grande and the resulting channel adjustments in both the vertical and lateral dimensions have altered the riparian and aquatic habitats. The floodplain is disconnected from the river channel and no longer floods at peak flows. Regeneration of the native cottonwood forest is affected and encroachment of nonnative vegetation is occurring. The channel pattern has shifted from a wide, braided configuration with mid-channel bars, to a single-thread straight and meandering planform (Richard & Julien, 2003).