This watershed is immense, the majority of it being within Canada.  In the U.S., the eastern two-thirds of massive Rainy Lake is part of the border lakes in Voyageurs National Park (VNP), as are adjacent Namakan and Sand Point Lakes. VNP also includes Kabetogama Lake. These four very large, interconnected lakes provide spectacular, undeveloped scenery, dotted with islands. Motor boats and other watercraft are allowed within the park and are the only practical means of entering this unique national park. Winter access is by snowmobile, dog sled or skis. This area is primarily boreal forest on shallow soils over bedrock or peat bog. This watershed’s eastern four-fifths is in the Border Lakes ecological sub-region; the western one-fifth is in the Little Fork / Vermilion Uplands interlaced with extensive wetland bogs. Wilderness recreation/tourism is the prime economic driver due to the scenic beauty, resorts, camping, fishing and hunting opportunities. Logging also occurs outside of the VNP.

The Rainy River Basin Plan, which included this watershed, was published in 2004 in partnership with local, county and other state agencies. Significant and successful collaborative efforts have been made with Canadian resource agencies and the International Joint Commission to manage the Rainy River Basin waters on both sides of the border. In 2017, the state’s Intensive Watershed Monitoring (IWM) ten-year cycle started and all major lakes in this watershed were determined to have a fish consumption advisory for mercury levels. MPCA scientists found that generally the streams in this watershed are in good condition, though there is some room for improvement and these waters must be preserved and protected to prevent future impairments. No reaches within the watershed are designated as impaired for aquatic life use; however, fish index of biological integrity and macroinvertebrate index of biological integrity scores are below their expected thresholds in a middle section of the Rat Root River, the largest river in the watershed. Aquatic life indicators, including total suspended solids (TSS) and dissolved oxygen (DO), frequently exceed state water quality (WQ) standards in parts of the watershed. For more information, please go to:

In Ontario, water quality data are collected here as part of the Broadscale Monitoring Program with data collected from a random sample of lakes in 2010 and 2016. The watershed is entirely bedrock with the soil being primarily a thin layer of glacial till. Overall, water quality conditions are good with lakes tending to have slightly lower water clarity and higher phosphorus than other Ontario watersheds.  The 2010 data indicate that average Secchi depth is 3.5 m, average total phosphorus is 10.2 ug/L and average pH is 7.1.

The Town of Atikokan (~2,500) as well as several smaller First Nation communities and lakes with cottaging development are found within the watershed with some localized water quality impairment associated with human activity. Logging and related road construction is the major land development activity.  The Seine River has hydroelectric development with three power generating facilities and several lakes dammed as reservoirs. Although there are no active mines, the watershed does contain the former Steep Rock mine site which has impaired water quality (notably high sulphate levels) contained on-site. Currently, there is no run off from the site and there is extensive rehabilitation work being done to address water concerns before the pit lakes fill and runoff to the surrounding watershed occurs.