.m .. Snake River Watershed Monitoring and Assessment Report October 2016 Authors Contributors/acknowledgements MPCA Snake River Watershed Report Team: Citizen Stream Monitoring Program Volunteers Anthony Dingmann, Michael Bourdaghs, The MPCA is reducing printing and mailing costs Andrew Butzer, Dave Christopherson, David by using the Internet to distribute reports and Duffey, Mark Gernes, Joseph Hadash, Michael information to wider audience. Visit our website Sharp, Nate Sather, Bruce Monson, Scott for more information. Niemela, Shawn Nelson, Denise Oakes, Kris Parson MPCA reports are printed on 100 percent post- consumer recycled content paper manufactured without chlorine or chlorine derivatives. Minnesota Department of Natural Resources Minnesota Department of Health Minnesota Department of Agriculture Middle-Snake-Tamarac Watershed District International Water Institute Project dollars provided by the Clean Water Fund (from the Clean Water, Land and Legacy Amendment). Minnesota Pollution Control Agency 520 Lafayette Road North | Saint Paul, MN 55155-4194 | www.pca.state.mn.us | 651-296-6300 Toll free 800-657-3864 | TTY 651-282-5332 This report is available in alternative formats upon request, and online at www.pca.state.mn.us Document number: wq-ws3-09020309b List of Acronyms AUID Assessment Unit Identification LRVW Limited Resource Value Water Determination M Mesotrophic CCSI Channel Condition and Stability Index MCES Metropolitan Council Environmental CD County Ditch Services Chl-a Chlorophyll-a MDA Minnesota Department of Agriculture CI Confidence Interval MDH Minnesota Department of Health CLMP Citizen Lake Monitoring Program M-IBI Macroinvertebrate Index of Biotic Integrity CR County Road MLRA Major Land Resource Area CSAH County State Aid Highway MNDNR Minnesota Department of Natural CSMP Citizen Stream Monitoring Program Resources CWA Clean Water Act MPCA Minnesota Pollution Control Agency CWLA Clean Water Legacy Act MSHA Minnesota Stream Habitat Assessment DO Dissolved Oxygen MTS Meets the Standard DOP Dissolved Orthophosphate MWP Mixed Wood Plains E Eutrophic MWS Mixed Wood Shield EPA U.S. Environmental Protection Agency N Nitrogen EQuIS Environmental Quality Information System Nitrate-N Nitrate Plus Nitrite Nitrogen E. coli Escherichia coli NA Not Assessed EXS Exceeds Criteria, Potential Severe NHD National Hydrologic Dataset Impairment NH3 Ammonia F-IBI Fish Index of Biotic Integrity NPDES National Pollution Discharge Elimination FS Full Support System FQA Floristic Quality Assessment NS Not Supporting FWMC Flow Weighted Mean Concentration NT No Trend H Hypereutrophic OP Orthophosphate HGM Hydrogeomorphically P Phosphorus HUC Hydrologic Unit Code PCB Polychlorinated Biphenyl IBI Index of Biotic Integrity PFC Perfluorochemicals IWI International Water Institute PFOS Perfluorooctane Sulfonate IWM Intensive Watershed Monitoring PMR Pesticide Monitoring Region IF Insufficient Information PWI Protected Waters Inventory K Potassium RNR River Nutrient Region LAP Lake Agassiz Plain SWAG Surface Water Assessment Grant ii SWCD Soil and Water Conservation District TALU Tiered Aquatic Life Uses TKN Total Kjeldahl Nitrogen TMDL Total Maximum Daily Load TP Total Phosphorus TSS Total Suspended Solids UAA Use Attainability Analysis USGS United States Geological Survey WMA Wildlife Management Area WPLMN Watershed Pollutant Load Monitoring Network iii Contents List of Acronyms ................................................................................................................................ ii Contents ........................................................................................................................................... iv List of Figures ..................................................................................................................................... v List of Tables .................................................................................................................................... vii Executive summary ............................................................................................................................8 Introduction ......................................................................................................................................9 I. The watershed monitoring approach ................................................................................................ 10 II. Assessment methodology .................................................................................................................. 17 III. Watershed overview .......................................................................................................................... 22 IV. Watershed-wide data collection methodology .................................................................................. 33 V. Individual HUC-11 subwatershed results ........................................................................................... 37 VI. Watershed-wide results and discussion ............................................................................................. 90 VII. Summaries and recommendations .................................................................................................. 114 Literature cited .............................................................................................................................. 117 Appendix 1 - Water chemistry definitions ....................................................................................... 120 Appendix 2 - Intensive watershed monitoring water chemistry stations in the Snake River Watershed ..................................................................................................................................... 122 Appendix 3 - AUID table of stream assessment results (by parameter and beneficial use) ................ 123 Appendix 4. Snake River Watershed IBI thresholds and results. ....................................................... 128 Appendix 4.1 - Minnesota statewide IBI thresholds and confidence limits .................................................. 128 Appendix 4.2 - Biological monitoring results – F-IBI (assessable reaches) ................................................... 129 Appendix 4.3 - Biological monitoring results – M-IBI (assessable reaches) ................................................. 131 Appendix 5 – Fish species found during biological monitoring surveys ............................................. 133 Appendix 6 – Macroinvertebrate species found during biological monitoring surveys. ..................... 135 iv List of Figures Figure 1. Minnesota's 80 major watersheds (8 Digit HUC Scale). ............................................................... 10 Figure 2. WPLMN monitoring sites in the Snake River Watershed. ........................................................... 11 Figure 3. The IWM design. .......................................................................................................................... 13 Figure 4. IWM sites for streams in the Snake River Watershed. ................................................................ 14 Figure 5. Monitoring location of local groups and citizens in the Snake River Watershed. ....................... 16 Figure 6. Flowchart of aquatic life use assessment process. ...................................................................... 21 Figure 7. Permitted feedlots and NPDES discharges within the Snake River Watershed .......................... 24 Figure 8. MLRA in the Snake River Watershed. .......................................................................................... 25 Figure 9. Land use in the Snake River Watershed....................................................................................... 27 Figure 10. Map of percent modified streams by major watershed (HUC-8). ............................................. 29 Figure 11. Comparison of natural to altered streams in the River Watershed .......................................... 29 Figure 12. State-wide precipitation levels during the 2013 water year. .................................................... 30 Figure 13. Precipitation trends in west central Minnesota (1993-2013) with five year running average. 31 Figure 14. Precipitation trends in west central Minnesota (1913-2013) with 10- year running average. 31 Figure 15. Western Province Generalized cross section (Source: MNDNR, 2001). .................................... 32 Figure 16. Average annual recharge rate to surficial materials in Snake River Watershed (1971-2000). .. 33 Figure 17. 2009-2013 hydrograph, sampling regime and annual runoff for the Snake River near Bigwoods, Minnesota. ................................................................................................................................ 34 Figure 18. Dam on the Snake River upstream of Warren during high (left) and low flows (right) and the location of the fish ladder (photos courtesy of MSTWD 2009). ................................................................. 46 Figure 19. Snake River PL-566 Flood Control impoundment located roughly 10 miles northeast of Warren (Photos courtesy of MSTWD 2009). ............................................................................................................ 47 Figure 20. Agassiz Valley Impoundment during high flows (left) and low water levels (right) .................. 47 Figure 21. Currently listed impaired waters by parameter and land use characteristics in the Snake River Subwatershed.........................................................................................................................