Watershed health July 2018 Winnebago River and Upper Wapsipinicon River Watersheds Monitoring and Assessment Report Authors The MPCA is reducing printing and mailing costs by using the Internet to distribute reports and Mel Markert, Joe Hadash, Joel Chirhart, Mark information to wider audience. Visit our Gernes, David Duffey, Mike Walerak, James website for more information. Jahnz, Tiffany Schauls, Justin Watkins, David Christopherson, Bruce Monson, Shawn Nelson MPCA reports are printed on 100% post- consumer recycled content paper Contributors/acknowledgements manufactured without chlorine or chlorine Citizen Stream Monitoring Program Volunteers derivatives. Minnesota Department of Natural Resources Minnesota Department of Health Minnesota Department of Agriculture Iowa Department of Natural Resources 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 | 651-296-6300 | 800-657-3864 | Or use your preferred relay service. | [email protected] This report is available in alternative formats upon request, and online at www.pca.state.mn.us. Document number: wq-ws3-07080203b Contents List of acronyms ....................................................................................................................................... v Executive summary .................................................................................................................................. 1 Introduction ............................................................................................................................................. 2 The watershed monitoring approach ............................................................................................................... 3 Assessment methodology ................................................................................................................................ 8 Watershed overview ...................................................................................................................................... 12 Watershed-wide data collection methodology .............................................................................................. 34 Individual aggregated 12-HUC subwatershed results ............................................................................... 38 Aggregated 12-HUC subwatersheds .............................................................................................................. 38 Headwaters Wapsipinicon River Aggregated 12-HUC HUC 0708010202-01 ......................................... 39 Lime Creek Aggregated 12-HUC HUC 0708020301-04 .......................................... 42 Watershed-wide results and discussion .................................................................................................. 48 Stream water quality ...................................................................................................................................... 48 Lake water quality .......................................................................................................................................... 49 Fish contaminant results ................................................................................................................................ 49 Pollutant load monitoring .............................................................................................................................. 50 Groundwater monitoring ............................................................................................................................... 55 Stream flow .................................................................................................................................................... 55 Wetland condition .......................................................................................................................................... 55 Summaries and recommendations .......................................................................................................... 68 Literature cited ...................................................................................................................................... 69 Appendix 1 – Water chemistry definitions ..................................................................................................... 72 Appendix 2.1 – Intensive watershed monitoring water chemistry stations in the Winnebago River Watershed Upper Wapsipinicon River Watershed ........................................................................................ 74 Appendix 2.2 – Intensive watershed monitoring biological monitoring stations in the Winnebago River watershed and Wapsipinicon River watershed .............................................................................................. 74 Appendix 3.1 – Minnesota statewide IBI thresholds and confidence limits .................................................. 75 Appendix 3.2 – Biological monitoring results – fish IBI (assessable reaches) ................................................ 76 Appendix 3.3 – Biological monitoring results-macroinvertebrate IBI (assessable reaches) .......................... 77 Appendix 4.1 – Fish species found during biological monitoring surveys ...................................................... 78 Appendix 4.2 – Macroinvertebrate species found during biological monitoring surveys ............................. 79 Appendix 5 – Minnesota Stream Habitat Assessment results ....................................................................... 84 i Figures Figure 1. The Intensive Watershed Monitoring Design. ....................................................................................... 4 Figure 2. Intensive watershed monitoring sites for streams in the Upper Wapsipinicon River watershed. ........ 6 Figure 3. Intensive watershed monitoring sites for streams in the Winnebago River watershed. ...................... 7 Figure 4. Flowchart of aquatic life use assessment process. .............................................................................. 11 Figure 5. The Winnebago River watershed within the Western Corn Belt Plains ecoregion of southern Minnesota. .......................................................................................................................................................... 14 Figure 6. The Upper Wapsipinicon River watershed within the Western Corn Belt Plains ecoregion of southern Minnesota. .......................................................................................................................................................... 15 Figure 7. Major Land Resource Areas (MLRA) in the Winnebago River watershed. .......................................... 16 Figure 8. Major Land Resource Areas (MLRA) in the Upper Wapsipinicon River watershed. ............................ 17 Figure 9. Land use in the Winnebago River watershed ...................................................................................... 19 Figure 10. Land use in the Upper Wapsipinicon River watershed. ..................................................................... 20 Figure 11. Map of percent modified streams by major watershed (8-HUC). ..................................................... 22 Figure 12. Comparison of natural to altered streams in the Upper Wapsipinicon River watershed (percentages derived from the Statewide Altered Water Course project). ............................................................................. 23 Figure 13. Comparison of natural to altered streams in the Winnebago River watershed (percentages derived from the Statewide Altered Water Course project). .......................................................................................... 24 Figure 14. Statewide precipitation total (left) and precipitation departure (right) during 2015 (DNR State Climatology Office, 2017a).................................................................................................................................. 25 Figure 15. Precipitation trends in Southeast Minnesota (1996-2015) with five-year running average (WRCC, 2017) ................................................................................................................................................................... 26 Figure 16 Precipitation trends in Southeast Minnesota (1916-2015) with ten-year running average (WRCC, 2017) ................................................................................................................................................................... 26 Figure 17. Locations of karst features in southeast Minnesota (Alexander, Yao & Green, 2006) ...................... 27 Figure 18. Locations of active status permitted high capacity withdrawals in the Upper Wapsipinicon and Winnebago watersheds (2015) ........................................................................................................................... 29 Figure 19. Total annual groundwater (above) and surface water (below) withdrawals in the Wapsipinicon and Winnebago watersheds (1996-2015) ................................................................................................................. 30 Figure 20 Distribution of wetlands according to the Minnesota updated National Wetland Inventory within the Winnebago and Upper Wapsipinicon watersheds. .....................................................................................