The DNR stocks walleye, northern pike, smallmouth bass, and trout in various parts of the watershed. Problems and Threats The Cannon River system and most other midwestern watersheds have been greatly altered from their natural state. The removal of natural vegetation, tiling and ditching of headwater sloughs, and the drainage of wetlands and beaver ponds have result in much faster runoff and more flooding and erosion. Soil and bank erosion bring excessive sediment into the river, where it damages habitats for both invertebrates and fish. The primary pollutants in the Cannon River Watershed are sediment, nutrients, toxic chemicals, and fecal bacteria.
Bottom sedimentation is the most common problem in the streams and rivers.
Nutrient overload is the reason for the algal blooms in the lakes, and nitrate from fertilizers and manure is a common groundwater pollutant. Toxic chemicals make certain types of fish unsuitable for frequent eating and have contaminated some groundwater supplies. High levels of fecal bacteria keep the rivers from supporting swimming during much of the summer. Ditching, draining, damming, stream straightening, bank clearing, paving. Farmland erosion, constructionsites, mining, urban runoff, stream bank erosion.