The Thief River and its tributaries have deteriorating water quality due to sedimentation. Sediment plumes and deltas have formed at the inlets of pools in Agassiz National Wildlife Refuge (Agassiz Pool) and Thief Lake, an important recreational resource in Northwest Minnesota.
Protecting groundwater aquifers that supply community drinking water supplies is critical for communities in Winona County. Well #219210 located within the Altura Drinking Water Supply Management Area (DWSMA) is an unused, multi-aquifer municipal well that poses a risk to the community drinking water supply. This well intersects with multiple aquifers, including the Prairie Du Chien, Jordan, Tunnel City/Lone Rock, and Wonewoc. These are primary aquifers used by the majority of drinking water wells in the region.