The EPA said most the nation's streams, rivers and other waters were in poor health.
EPA analysis said that 27 percent of the nation's waterways have high levels of nitrogen and 40 percent have high levels of phosphorus. Those chemicals lead to algae blooms that can deprive water of oxygen.
In terms of mercury, potentially harmful to developing nervous systems, the EPA said that more than 13,000 miles of rivers contained fish species with elevated levels in the systems.
For bacteria, about 9 percent of the nation's rivers and streams were considered unsafe for swimming while vegetation, which can help filter out pollutants, was down in about 24 percent of the waters monitored by the EPA.
"The health of our nation's rivers, lakes, bays and coastal waters depends on the vast network of streams where they begin, and this new science shows that America's streams and rivers are under significant pressure," Acting Assistant Water Administrator Nancy Stoner said in a statement.