What are the water quality problems?
The Rush River flows into the Minnesota River near Henderson. The Minnesota River, its tributaries, and the lakes within its drainage basin are prime natural resources for the state of Minnesota and for residents living within the watershed. It offers beautiful scenery, a bountiful population of migratory waterfowl, habitat for wildlife and opportunities for fishing and boating. In addition, surface water and groundwater aquifers provide drinking water for several communities and many rural residents.

Unfortunately, the extent of these benefits is limited by poor water quality, which is caused by:

Bacteria and other pathogens make river water unsafe for drinking and activities that involve body contact. These organisms may contain pathogens, which can cause disease.

Sedimentation restricts the areas where fish can spawn, limits biological diversity and keeps river water cloudy, reducing the growth of healthy plant life rooted in river beds.

Phosphorus pollution triggers the growth of huge populations of algae. Especially during times of low flow, in slow-flowing areas such as reservoirs and the lower reaches of the Minnesota River, these high rates of algae growth can severely deplete the supply of oxygen in the river, endangering fish and other kinds of aquatic life.

Nitrate-Nitrogen pollutes water in the Minnesota River, which recharges aquifers used for drinking water at Mankato. In addition, nitrate-nitrogen from the Minnesota River contributes to hypoxia in the Gulf of Mexico by stimulating the growth of algae which, through death and decay, consume large amounts of dissolved oxygen and thereby threaten aquatic life.

Hydrologic Modification, in addition to water quality, also is a concern that limits the beneficial uses of rivers and streams within the Minnesota River basin. Chronic annual floods can downcut and widen streams, damage property and place severe stress on communities and individual residents of the floodplain. Typically, those living in the lower reaches of the watershed may be economically impacted by extensive drainage up the watershed.

Downstream Impacts
In addition, poor water quality in the Minnesota River Basin can contribute to problems experienced downstream. One example is the problem of excessive algae growth in Lake Pepin, which is particularly severe in dry, low-flow years. Phosphorus discharged from the Minnesota into the Mississippi River has been identified as a significant source of Lake Pepin's problem. Further downstream, where the Mississippi River enters the Gulf of Mexico, excess nitrogen from the river has been identified as contributing to high rates of algae growth, and subsequent oxygen depletion when the algae die and decompose. The Minnesota River has been identified as one of several relatively high contributors of nitrogen into the Mississippi River. Thus, it is may be at least partly responsible for this problem.

Text courtesy of Minnesota Pollution Control Agency (MPCA)
http://www.pca.state.mn.us/water/basins/mnriver/