Downstream water quality impacts pose a significant concern. When the High Island Creek reaches the Minnesota River and than into the Mississippi River, the water carries excess nutrients and sediment. Therefore, the High Island Creek and Minnesota River contributes to the broader Mississippi River water quality problems, specifically in Lake Pepin and the Northern Gulf of Mexico.

Elevated phosphorus and sediment are a particular concern for Lake Pepin. The lake is filling in at a quicker-than-natural pace due to large sediment loads depositing on the lake bed. Lake Pepin also has a problem with excessive algae blooms during low-flow years due to elevated phosphorus levels, some of which have resulted in fish kills.

Further downstream, where the Mississippi drains into the Gulf of Mexico, excess nitrogen from the Minnesota River contributes to low-oxygen problems that impact aquatic life. Researchers have estimated that the Upper Mississippi Watershed contributes more than 30 percent of the annual Nitrogen load to the Mississippi. The zone of hypoxia or dead zone is an area devoid of marine life stretching from the Mississippi River to as far as Texas. Each summer excess nutrients trigger massive algal blooms which result in decreased dissolved oxygen levels. When oxygen in the water is depleted, fish, shrimp and other species can't survive. Local economies dependent upon these resources are crippled.

Source: State of the Minnesota River 2001 Report