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Biological Condition Index Development for the Truckee River: Benthic Macroinvertebrate Assemblage

Prepared By

Tetra Tech, Inc.
10045 Red Run Blvd, 110
Owings Mills, MD 21117

Prepared For

Nevada Division of Environmental Protection
July 2004


The objective of our analysis was to develop a biological index for benthic macroinvertebrates for the Nevada portion of the mainstem of the Truckee River using preexisting data. We analyzed data collected by four separate entities, Nevada Division of Environmental Protection (NDEP), Pyramid Lake Paiute Tribe (PLPT), Truckee Meadows Water Reclamation Facility (TMWRF), and Desert Research Institute (DRI). To develop a common dataset from collections of multiple entities, an evaluation of the field and/or lab methodological differences was performed to minimize non-random error. A common index period was designated as low flow (July to October), all replicates were combined, and the number of individuals per sample was set to 500 organisms (samples with more organisms were randomly sampled with a computer to 500).

A multimetric index was developed from the data set and comprised six metrics or attributes of the benthic macroinvertebrate assemblage; total taxa, percent Ephemeroptera, percent Chironomidae, percent dominant taxon, percent filterers, and percent clingers. In an assessment, each metric value is converted to a standard score ranging between 0 and 100 (100 being closest to reference or optimal value). The scores for all six metrics are averaged to obtain an aggregated index score and compared to thresholds or break points based on percentages of the overall score and expected conditions for a good quality benthic macroinvertebrate community. Application of the benthic index to the mainstem of the Truckee River indicated the biological condition was of higher quality in the upper reaches and declined in quality as the river approaches Pyramid Lake. A more definitive assessment is pending the results of the analyses on companion assemblages of the aquatic community, namely the fish and algal assemblages.

Biological Condition Index Development for the Truckee River: Periphyton Assemblage

Prepared By
Clinton J. Davis and Christian H. Fritsen
Desert Research Institute
2215 Raggio Parkway
Reno NV, 89512

Prepared For
Nevada Division of Environmental Protection
February 6, 2006

The objectives of the current activities were to determine if sufficient data was available to derive preliminary periphyton-based metrics that could be used in a periphyton-based indices of ecological condition for the Lower Truckee River, which could in turn be used to derive more comprehensive indices of biological integrity (IBI) based on fish, macroinvertebrates and periphyton populations. Derivation of metrics and indices was made possible through the use of relatively recent (2000 to 2004) seasonal periphyton data that was collected from 11 to 15 locations from California-Nevada border to Pyramid Lake. Although, the levels of taxonomic information from the different data sets were not always comparable, several candidate metrics and indices encompassing information from both the species level and the genera level were identified, calculated and evaluated.

Notable among the metrics most amenable for a Truckee River Periphyton Index were the Siltation Index, Shannon Diversity Index, Eutraphentic Index, Diatom Generic Richness, % Achnanthes minutissima, Chlorophyll a and Ash Free Dry Weight. These metrics covered several aspects of the periphyton community characteristics (richness, composition, tolerance, and habit) that are desired attributes to be accounted for in multimetric indices.

Application of a periphyton-based multimetric index to the mainstem of the Truckee River indicates a general upstream to downstream trend for decreasing ecological condition. However, these results are based on a limited amount of periphyton data and also need to be evaluated in combination with Index’s for fishes and macroinvertebrates in order to gain a more complete picture of the “condition” of the lower Truckee River.

Truckee River Water Quality: Current Conditions and Trends Relevant to TMDLs and WLAs

Prepared for
Truckee Meadows Water Reclamation Facility
City of Reno and City of Sparks, Nevada

Prepared by
Alan Jassby PhD, Ted Daum MS, and Charles Goldman PhD
Ecological Research Associates
Davis, Calif.
September 10, 2007


Sedimentation and Erosion in the Upper Truckee River and Trout Creek Watershed (1969)

Dept. of Conservation
Division of Source Conservation

This report on erosion, sedimentation, and flooding on the Trout Creek and Upper Truckee River Watershed is based on field work carried out by the Division of Soil Conservation. It is a part of a larger study, the Lake Tahoe Coordinated Study, initiated by the Department of Conservation in 1967 which involved the Division of Soil Conservation, the Division of Mines and Geology, and the Division of Forestry. The coordinated study is intended to help agencies of local government and others to cope with resource problems that have developed within the Lake Tahoe Basin.

Truckee River Water Chemistry Synoptic Study

Prepared by
Carollo Engineers with Assistance from Rapid Creek Research

As part of the Truckee River watershed Coordinated Monitoring Program (CMP), intensive monitoring of Truckee River water quality was conducted in November 1998 with participation from many of the resource agencies in the area. The purposes of this report are to present the objectives of this study, summarize sampling protocols and laboratory procedures, present the data collected, and provide a brief discussion on the results and recommendations for future synoptic studies.

Preliminary Assessment of Contaminants and Potential Effects to Fish of the Truckee River, Nevada

Written By
Damian K. Higgins, Peter L. Tuttle, and J. Scott Foote
U.S. Fish and Wildlife Service
Nevada Fish and Wildlife Office

Environmental Contaminants Program
Off-Refuge Investigations Sub-Activity
FFS # 1130-1F35

January 2006

Previous investigations by U.S. Geological Survey (USGS) and others reported elevated concentrations of a variety of metals and polycyclic aromatic hydrocarbons (PAH) in Truckee River sediment collected in and downstream of the Reno-Sparks metropolitan area in Nevada in 1998. USGS scientists also documented elevated contaminant concentrations in fish and aquatic invertebrates which exceeded published biological effects criteria. In 1999 U.S. Fish and Wildlife Service (Service) biologists also noted a higher incidence of lesions, hemorrhagic septicemia, and external parasites in fish collected in this same reach. Therefore, the Service initiated a synoptic investigation in 2002 to determine if contaminants are affecting or have the potential to affect fish health, survival, or reproductive potential in the lower Truckee River. Specific Service objectives included: 1) evaluation of fish abundance and community structure; 2) assessment of the external condition of fish; 3) detailed evaluation of salmonid health (i.e., internal/external condition, histology, cytology, disease, and parasites); 4) characterization of fish contaminant exposure and accumulation; and 5) screening for indicators of endocrine disruption.

Fish were collected from 5 sampling sites on the Truckee River from Verdi, Nevada to its terminus near the Marble Bluff Dam at Pyramid Lake. Abundance and community structure values (species evenness and Index of Biotic Integrity) declined in a downstream fashion with notable reductions occurring at the Lockwood and Marble Bluff sample sites which were likely a result of cumulative effects of urbanization, loss of riparian cover, reduced flows, increased water temperature, as well as contaminants. Condition of brown trout and mountain/Tahoe suckers were significantly reduced at downstream sites. High percentages of external anomalies were also observed at sampling sites downstream of the Reno-Sparks urban area and ranged from 11% at Marble Bluff to a maximum of 43% at Lockwood. These anomalies were also likely the result of non-point sources, sewage effluent discharges, and reduced flows.

Evaluations of salmonid health revealed no significant issues with regards to organosomatic assays, blood chemistry, microbiological assessment, and histological evaluation from each sampling site. However, some data indicated suspected infections of bacterial kidney disease and other bacterial-type infections. However, these infections were not expressive enough or had detrimental impacts to those fish.

To assess contaminant exposure and accumulation, five to seven trout of appropriate size (? 200 mm) were randomly selected from sampling sites and were analyzed for polycyclic aromatic hydrocarbon metabolites in bile and concentrations of metals or trace elements in whole fish. Bile data revealed fish were being exposed to elevated concentrations of naphthalene and phenanthrene in the Reno-Sparks area. These concentrations, which were likely the result of urban run-off sources, exceeded criteria considered as contaminated. Whole fish data revealed concentrations of aluminum, barium, iron, and manganese were highest in rainbow trout compared to brown trout. Mercury concentrations in brown trout did not exceed water quality standards established by the Pyramid Lake Paiute Tribe. Concentrations of aluminum and barium in whole fish were highest above Reno and were likely the result of geochemical interactions of stream water with specific bedrock types. However, none of these concentrations exceeded known adverse biological effects. Concentrations of arsenic, mercury, and selenium in whole fish were highest at the Tracy sampling site located below the Reno-Sparks urban area. The sources of uptake for these constituents originate mostly from geothermal springs, historic mine wastes, irrigation, and tertiary-treated sewage effluent within the Steamboat Creek drainage. Arsenic and selenium concentrations did not exceed known adverse biological effects. Mercury concentrations in trout downstream of the Reno-Sparks urban area did not exceed avian dietary effects, fish consumption guidelines, and water quality standards established by the Pyramid Lake Paiute Tribe.

Several studies have associated municipal waste water discharges with endocrine system effects in fish. Because treated municipal waste water represents a significant component of flows in the lower Truckee River, blood plasma was collected to screen for indicators of endocrine disruption in trout. Vitellogenin (VTG) concentrations were detected in two males downstream of the Reno-sparks urban area. Male fish do not normally produce VTG, but the hepatic estrogen receptor and the gene that encodes for VTG is still present. The result is that when male fish are exposed to estrogenic compounds, VTG production can be induced. Also, all adult males in the fish health assessment had no mature testes at all sites. The presence of VTG in the two males combined with the organosomatic data provides some evidence of potential endocrine disruption in individual trout. However, additional research is needed to assess which endocrine disrupting compounds may be present in the Truckee River, and the extent to which these compounds may be affecting fish populations.

The long-term health and reproductive potential of fish in the Truckee River will be increasingly affected as the Reno-Sparks urban area continues to expand. Restoration of river function and augmentation of wetlands within the floodplain would assist in attenuating contributions of contaminants from various point and non-point sources. Improvements in sewage effluent discharges and effective urban planning can also assist to reduce both point and non-point sources of some contaminants. Without addressing these issues, these point and non-point sources of contaminants will present significant challenges to maintaining a healthy fishery and prevent long-term restoration efforts of Lahontan cutthroat trout (Oncorhynchus clarki henshawi) in the Truckee River.

Written in cooperation with

The authors acknowledge members of the U.S. Fish and Wildlife Service, U.S. Geological Survey, Nevada Department of Wildlife, Pyramid Lake Paiute Tribe and University of Nevada, Reno for providing ideas and information on fish and water-quality issues and for participating in this study. Members of those organizations who participated in data collection and provided technical assistance for this study include:

U.S. Fish and Wildlife Service
William Cowan, Jody Fraser, Rick Harmon, Chad Mellison, Bridget Nielsen, Stan Wiemeyer

U.S. Geological Survey
Timothy S. Gross, Angela Paul, Timothy Rowe, Karen A. Thomas

Nevada Department of Wildlife
Kim Tisdale

Pyramid Lake Paiute Tribe
Beverly Harry, Dan Mosley, Nancy Vucinich

University of Nevada, Reno
Sudeep Chandra, Ph.D, Laurel Saito, Ph.D

Total Maximum Daily Loads (TMDLs) and Waste Load Allocations (WLAs) Final Report, February 1994

Section 303(d) of the Clean Water Act requires states to identify waters that do not or are not expected to meet applicable water quality standards with technology-based controls alone. Once these waters are identified, states are to develop total maximum daily loads (TMDLs) at a level necessary to achieve the applicable water quality standards. The Truckee River at Lockwood is listed on Nevada's 303(d) List for total nitrogen, total phosphorus and total dissolved solids. NDEP has chosen to use the chemical specific approach for the establishing TMDLs.

Section 303(d) of the Clean Water Act requires states implement water quality-based controls where technology based limits and implemented Best Management Practices (BMPs) are not sufficient to achieve water quality standards. A TMDL is a tool for implementing State water quality standards and is based on the relationship between pollutant sources and in-stream water quality conditions. TMDLs integrate the management of both point and nonpoint sources of pollution to a waterbody. The TMDL establishes the allowable loadings or other quantifiable parameters for a waterbody and thereby provides the basis for establishing water quality-based controls. These controls should provide the pollution reduction necessary for a waterbody to meet water quality standards.

A TMDL quantifies pollutant sources and allocates allowable loads to the contributing point and nonpoint sources so that the water quality standards are attained. The greatest amount of loading that a water can receive without violating water quality standards is the loading capacity. The waste load allocation (WLA) is the portion of a receiving water's loading capacity that is allocated to existing or future point sources of pollution. EPA regulations (40 CFR 130.2(g)) provide that load allocations for nonpoint sources and/or natural background "are best estimates of the loading which may range from reasonably accurate estimates to gross allotments...."

This document first describes the methodology used for determining a TMDL for both conservative and nonconservative parameters. Then water quality attainment programs other than waste load allocations in the Truckee Meadows Water Reclamation Facility (formerly known as the Reno/Sparks Wastewater Treatment Facility) NPDES permit are discussed. Finally, TMDLs/WLAs for TDS, TN and TP are discussed including a discussion of the proposed NPDES permit and attainability.

Load Duration Curve Methodology for Assessment and TMDL Development Nevada Division of Environmental Protection

The major streams in Nevada have had TMDLs (Total Maximum Daily Loads) established for several years. However for some of these streams, the TMDLs are expressed as an average daily load based upon average long term flow conditions. These TMDLs have been dubbed as "bare bones" TMDLs due to the simplicity of the calculation and their lack of usefulness. While these TMDLs seem to satisfy the requirements of the Clean Water Act, they have contributed little to any watershed/waterbody assessment and restoration plans. These types of TMDLs do little to characterize the problems the TMDLs are intended to address. Without adequate characterizations, appropriate solutions cannot be identified and implemented.

Evaluation of Groundwater and Solute Transport in the Fernley – Wadsworth Area

The Truckee River Water Quality Agreement of 1997 settled longstanding litigation between the Pyramid Lake Paiute Tribe (PLPT) and the U.S. Environmental Protection Agency (EPA), State of Nevada and the Cities of Reno and Sparks (“Cities”), respectively. A key element of this agreement was a commitment by the Cities and the Department of the Interior to spend up to $24 million to purchase Truckee River water rights from downstream of Sparks. Water would subsequently be sorted in upper basin reservoirs for release under low-flow conditions to help the Cities meet water quality objectives, particularly those related to nutrients and dissolved oxygen. It was further anticipated that a reduction in irrigated agriculture within the Fernley area would result in an associated decrease in high total dissolved solids (TDS) groundwater discharge to the river, helping to mitigate salinity loading to Pyramid Lake.

A hydrogeologic investigation was undertaken to characterize the groundwater system in the Fernley Basin and to determine the TDS loading to the Truckee River between the towns of Wadsworth and Nixon. A groundwater flow and transport model was constructed to integrate all of the available data and to predict the potential loadings under various management alternatives.

Biological Condition Index Development for the Lower Truckee River and Eastern Sierra Nevada Rivers: Fish Assemblage

Written By

Robert M. Hughes and Thomas R. Whittier
Department of Fisheries and Wildlife
Oregon State University
200 SW 35th Street
Corvallis, Oregon 97333
Gregg A. Lomnicky
Dynamac Corporation
200 SW 35th Street
Corvallis, Oregon 97333

Prepared For
Pyramid Lake Paiute Tribe
Nevada Division of Environmental Protection
April 2005
We developed a fish assemblage IBI for western Nevada rivers and applied it to the Truckee River. Available state and federal fish assemblage data from the Carson, Walker, and upper Truckee rivers were analyzed to select and score metrics. Selected metrics included number of native species, % sculpin individuals, % mountain whitefish individuals, evidence of sculpin and whitefish reproduction, % cutthroat trout individuals, % sensitive individuals, % mountain sucker individuals, % omnivorous individuals, % highly tolerant individuals, % alien individuals, and % external anomalies. Metrics were scored continuously from 0-1 and the IBI was scored from 0-10 by summing the metrics. Those metrics and scoring criteria were then applied to existing fish assemblage data for the lower Truckee River. The IBI declined from the Nevada border to Wadsworth, with sharp declines at river miles 57 (Oxbow), 69 (Mustang), and 87 (Painted Rock). Revisits to the same sites indicated that IBI scores may vary by 1.0 as a result of temporal and sampling variation. We consider median IBI scores >7.5 as acceptable, 5.0-7.4 as marginally damaged, and <5.0 as damaged. However, these are only guidelines and 2.0 changes in IBI scores over space or time are probably biologically significant.

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