Watershed health June 2020 Rainy River – Rainy Lake Watershed Monitoring and Assessment Report Author Nathan Mielke Contributors/acknowledgements Jordan Donatell, Benjamin Lundeen, Sophia Vaughan, Michael Bourdaghs, Bruce Monson, Stacia Grayson, Kelli Nerem, Jenny Jasperson, Amy Mustonen Minnesota Department of Natural Resources Minnesota Department of Health Koochiching County SWCD A.W. Research Laboratories Editing and graphic design Scott Niemela, Lee Engel, Pam Anderson 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-ws3-09030003b Contents Contents ........................................................................................................................................... i Tables .............................................................................................................................................. iii Figures ............................................................................................................................................. iv List of acronyms .............................................................................................................................. vi Executive summary ......................................................................................................................... 1 Introduction .................................................................................................................................... 2 The watershed monitoring approach ..................................................................................................3 Assessment methodology ..................................................................................................................7 Watershed overview ....................................................................................................................... 11 Watershed-wide data collection methodology .................................................................................. 33 Individual aggregated 12-HUC subwatershed results .................................................................. 37 Aggregated 12-HUC subwatersheds ................................................................................................. 37 Rat Root River Aggregated 12-HUC HUC 0903000318-01 .............................. 38 Rat Root River, East Branch Aggregated 12-HUC HUC 0903000318-02 .............................. 42 Rainy Lake Aggregated 12-HUC HUC 0903000319-01 .............................. 45 Watershed-wide results and discussion ....................................................................................... 49 Stream water quality ....................................................................................................................... 49 Lake water quality ........................................................................................................................... 50 Biological monitoring ...................................................................................................................... 51 Fish contaminant results .................................................................................................................. 52 Pollutant load monitoring ................................................................................................................ 56 Stream flow .................................................................................................................................... 59 Wetland condition ........................................................................................................................... 60 Transparency trends for the Rainy River – Rainy Lake Watershed ....................................................... 67 Priority waters for protection and restoration in the Rainy River – Rainy Lake Watershed .................... 67 Summaries and recommendations ............................................................................................... 69 Literature cited.............................................................................................................................. 71 Appendix 1 – Water chemistry definitions ......................................................................................... 74 Appendix 2-Intensive watershed monitoring water chemistry stations in the Rainy River–Rainy Lake Watershed ................................................................................................................................... 76 Appendix 3 - Intensive watershed monitoring biological monitoring stations in the Rainy River – Rainy Lake Watershed............................................................................................................................ 76 Appendix 4 - Other biological monitoring stations in the Rainy River – Rainy Lake Watershed .............. 76 Appendix 5 – Minnesota statewide index of biological integrity (IBI) thresholds and confidence limits .. 77 i Appendix 6 - Biological monitoring results - fish IBI ............................................................................ 78 Appendix 7 - Biological monitoring results - macroinvertebrate IBI ..................................................... 78 Appendix 8 – Fish species found during biological monitoring ............................................................ 79 Appendix 9 – Macroinvertebrate species found during biological monitoring ...................................... 80 Appendix 10 – Minnesota stream habitat assessment results for the Rainy River – Rainy Lake Watershed .................................................................................................................. 82 Appendix 11 – Lake protection and prioritization results .................................................................... 83 ii Tables Table 1. Tiered aquatic life use standards. ................................................................................................... 8 Table 2. Aquatic life and recreation assessments on stream reaches: Rat Root River Aggregated 12-HUC. Reaches are organized upstream to downstream in the table. ................................................................. 38 Table 3. Aquatic life and recreation assessments on stream reaches: Rat Root River, East Branch Aggregated 12-HUC. Reaches are organized upstream to downstream in the table. ................................ 42 Table 4. Lake assessments: Rainy Lake Aggregated 12-HUC. ..................................................................... 46 Table 5. Assessment summary for stream water quality in the RRRL Watershed. .................................... 50 Table 6. Assessment summary for lake water chemistry in the RRRL Watershed. .................................... 50 Table 7. Fish contaminants: summary of fish length, mercury, PCBs, and PFOS by waterway-species-year. .................................................................................................................................................................... 53 Table 8. WPLMN stream monitoring site for the RRRL Watershed. ........................................................... 56 Table 9. Water clarity trends. ..................................................................................................................... 67 iii Figures Figure 1. The Intensive Watershed Monitoring (IWM) design. .................................................................... 4 Figure 2. Intensive watershed monitoring stations for streams in the RRRL Watershed............................. 5 Figure 3. Monitoring locations of local groups, citizens and the MPCA monitoring staff in the RRRL Watershed..................................................................................................................................................... 6 Figure 4. Flowchart of aquatic life use assessment process. .......................................................................... Figure 5. The RRRL Watershed and the portion within Minnesota. ........................................................... 11 Figure 6. The RRRL Watershed within the Northern Minnesota Wetlands and the Northern Lakes and Forests ecoregion of Minnesota. ................................................................................................................ 12 Figure 7. Approximate total extent of Lake Agassiz over 5,000 years in relation to the RRRL Watershed. .................................................................................................................................................................... 13 Figure 8. Major Land Resource Areas (MLRA) in the RRRL Watershed. ..................................................... 15 Figure 9. Land ownership in the RRRL Watershed. ..................................................................................... 19 Figure 10. Land cover in the RRRL Watershed. ........................................................................................... 20 Figure 11. Comparison of natural to altered streams in the RRRL Watershed (percentages derived from the state-wide altered water course project). ...........................................................................................