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Ecological Risk Assessment for the Middle Snake River, Idaho

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Ecological Risk Assessment for the Middle Snake River, Idaho United States Office of Research and EPA/600/R-01/017 Environmental Protection Development February 2002 Agency Washington, DC 20460 Ecological Risk Assessment for the Middle Snake River, Idaho National Center for Environmental Assessment—Washington Office Office of Research and Development U.S. Environmental Protection Agency Washington, DC EPA/600/R-01/017 February 2002 ECOLOGICAL RISK ASSESSMENT FOR THE MIDDLE SNAKE RIVER, IDAHO U.S. Environmental Protection Agency National Center for Environmental Assessment-Washington Office Office of Research and Development Washington, DC Office of Environmental Assessment Region 10 Seattle, Washington DISCLAIMER This document has been reviewed in accordance with U.S. Environmental Protection Agency policy and approved for publication. Mention of trade names or commercial products does not constitute endorsement or recommendation for use. ABSTRACT An ecological risk assessment was completed for the Middle Snake River, Idaho. In this assessment, mathematical simulations and field observations were used to analyze exposure and ecological effects and to estimate risk. The Middle Snake River which refers to a 100 km stretch (Milner Dam to King Hill) of the 1,667 km long Snake River lies in the Snake River Plain of southern Idaho. The contributing watershed includes 22,326 square km of land below the Milner Dam and adjacent to the study reach. The demands on the water resources have transformed this once free-flowing river segment to one with multiple impoundments, flow diversions, significant alterations to river habitat, loss of native macroinvertebrate species, extirpation of native fish species, expansion of pollution-tolerant organisms, and excessive growth of macrophytes and algae. The environmental management goals for this assessment are:“attainment of water quality standards, establishment of total maximum daily loads for major pollutants, water for hydropower, recreation, and irrigation, recovery of endangered species, and sustained economic well being.” The diversity, reproduction, growth, and survival of representative species from three major trophic levels (fish, invertebrates, and plants) were chosen as assessment endpoints in order to complete an ecosystem level analysis. Simulation of habitat conditions (temperature, water velocity, and water depth) and review of field studies show that most spawning, rearing, and adult habitats available to native fish species and in the Middle Snake River are undesirable. In addition to high water temperatures, our analysis showed that low flows and sedimentation are main stressors affecting these fish species. These same factors are thought to be responsible for the decline of native snail populations. Risks of eutrophication were estimated by changes in the plant biomass. The simulation of macrophyte growth, under existing conditions in the study reach, indicates the river is eutrophic based on aquatic plant biomass exceeding 200 g/m2. The lines of evidence drawn from the model simulation suggest that nutrients, temperature, flow, and water depth are the major factors controlling macrophyte growth. Preferred citation: U.S. EPA (Environmental Protection Agency). (2001) Ecological risk assessment for the Middle Snake River, Idaho. National Center for Environmental Asssessment, Washingotn, DC; EPA/600/R-01/017. Available from: National Technical Information Service, Springfield, VA; PB___________and http://www.epa.gov/ncea. ii CONTENTS List of Tables ............................................................... vii List of Figures ............................................................... ix Foreword ................................................................... xi Preface .................................................................... xii Authors, Contributors, and Reviewers ............................................ xiii Acknowledgments ........................................................... xv 1. EXECUTIVE SUMMARY ................................................. 1-1 1.1. INTRODUCTION .................................................... 1-1 1.2. PLANNING ........................................................ 1-3 1.3. PROBLEM FORMULATION .......................................... 1-3 1.4. ANALYSIS ......................................................... 1-4 1.5. RISK CHARACTERIZATION ......................................... 1-5 2. INTRODUCTION ........................................................ 2-1 3. PLANNING ............................................................. 3-1 4. PROBLEM FORMULATION ............................................... 4-1 4.1. METEOROLOGY ................................................... 4-1 4.2. GEOLOGY ......................................................... 4-1 4.3. HYDROLOGY ...................................................... 4-8 4.4. DEMOGRAPHICS AND LAND USE ................................... 4-10 4.5. FISH POPULATIONS ............................................... 4-12 4.6. BENTHIC MACROINVERTEBRATES ................................. 4-13 4.7. AQUATIC PLANT COMMUNITIES ................................... 4-14 4.8. ASSESSMENT ENDPOINTS ......................................... 4-15 4.9. DECISION PATHWAY .............................................. 4-16 4.10. CONCEPTUAL MODEL ............................................. 4-17 4.11. LAND-USE ACTIVITIES THAT ALTER ECOSYSTEMS .................. 4-18 4.11.1. Twin Falls Sewage Treatment Plant .............................. 4-19 4.11.2. Confined Animal Feeding Operations ............................. 4-19 4.11.3. Aquaculture ................................................. 4-19 4.11.4. Irrigated Agriculture and Cattle Grazing ........................... 4-20 4.11.5. Nutrient and Sediment Loading .................................. 4-22 4.11.6. Impoundments ............................................... 4-22 4.11.7. Other Nonpoint Sources ....................................... 4-24 4.12. ECOSYSTEM DYNAMICS .......................................... 4-24 4.12.1. Water Column Dynamics ...................................... 4-25 4.12.2. Sediment Dynamics ........................................... 4-29 4.12.3. Dynamics of the Benthic Plant Community ........................ 4-31 5. SIMULATION OF ECOLOGICAL RISK ..................................... 5-1 5.1. QUANTITATIVE MEASURES OF EFFECT .............................. 5-1 iii CONTENTS (continued) 5.1.1. Water Quality Standards ........................................ 5-1 5.1.2. Habitat Suitability Indices ....................................... 5-3 5.2. RISK ESTIMATES ................................................... 5-6 5.2.1. Exceedance of Water Quality Standards ............................ 5-6 5.2.2. Habitat Suitability Indices ....................................... 5-9 6. ANALYSIS OF EXPOSURE AND EFFECTS FOR THREE FISH POPULATIONS .... 6-1 6.1. RAINBOW TROUT (Oncorhynchus mykiss) ............................... 6-1 6.1.1. Spawning Habitat ............................................. 6-2 6.1.2. Rearing Habitat ............................................... 6-2 6.1.3. Adult Habitat ................................................. 6-3 6.1.4. Overwintering Habitat .......................................... 6-4 6.1.5. Discussion ................................................... 6-4 6.2. MOUNTAIN WHITEFISH (Prosopium williamsoni) ........................ 6-5 6.2.1. Loss and Alteration of Lotic Habitat ............................... 6-6 6.2.2. Effects on Movement .......................................... 6-7 6.2.3. Effects on Spawning Activities ................................... 6-8 6.2.4. Loss and Alteration of Rearing Areas .............................. 6-9 6.2.5. Effects Due To an Altered Food Source and Prey Base ............... 6-10 6.2.6. Discussion .................................................. 6-13 6.3. WHITE STURGEON (Acipenser transmontanus) .......................... 6-14 6.3.1. Loss and Alteration of Lotic Habitat .............................. 6-15 6.3.2. Effects on Movement ......................................... 6-16 6.3.3. Effects on Spawning Activities .................................. 6-17 6.3.4. Predation on Eggs and Larvae ................................... 6-20 6.3.5. Loss and Alteration of Rearing Areas ............................. 6-21 6.3.6. Effects Due to an Altered Food Source and Prey Base ................ 6-22 6.3.7. Loss of Genetic Diversity ...................................... 6-24 6.3.8. Discussion .................................................. 6-25 7. ANALYSIS OF EXPOSURE AND EFFECTS FOR MACROINVERTEBRATES ..... 7-1 7.1. OVERVIEW ........................................................ 7-1 7.2. SAMPLING BY IDAHO STATE UNIVERSITY 1992-1994 .................. 7-1 7.3. STATUS OF THREATENED AND ENDANGERED MOLLUSCS IN THE MIDDLE SNAKE RIVER ........................... 7-7 7.3.1. Bliss Rapids Snail (Taylorchoncha serpenticola) ..................... 7-7 7.3.2. Idaho Springsnail (Pyrgulopsis idahoensis) ......................... 7-8 7.3.3. Snake River Physa (Physa natricina) .............................. 7-9 7.3.4. Utah Valvata (Valvata utahensis) ................................ 7-10 7.3.5. Banbury Springs Lanx (Lanx sp.) ................................ 7-11 8. ANALYSIS OF EXPOSURE AND EFFECTS FOR AQUATIC PLANTS ............ 8-1 8.1. HISTORIC TRENDS ................................................. 8-1 8.1.1. Phytoplankton ................................................ 8-2 iv CONTENTS (continued) 8.1.2. Vascular
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