Of the samples taken by government scientists, 25 percent contained mercury levels exceeding what the Environmental Protection Agency considers to be safe for average human consumption.
"This science sends a clear message that our country must continue to confront pollution, restore our nation's waterways, and protect the public from potential health dangers," Interior Secretary Ken Salazar said in a statement.
The study spanned seven years, from 1998 to 2005, and examined bed sediment, water and more than 1,000 fish. The types of fish included in the research were bass, trout and catfish.
Some of the highest levels of mercury in fish were found in the so-called "blackwater" streams in southern states including North Carolina, South Carolina, Georgia, Florida and Louisiana. The streams in question are in areas which contain wetlands.
High levels of mercury in fish also were found in relatively undeveloped watersheds in the Northeast and the Upper Midwest.
As for the Western states, elevated levels of mercury were found in areas where gold and mercury are being mined.
Atmospheric mercury is the main source of mercury to natural waters. Coal-fired power plants are the largest source of mercury emissions in the United States.
The sample with the highest concentration of mercury was taken from a smallmouth bass collected from the Carson River at Dayton, Nev. Gold mining takes place in the area.
All 50 states have mercury monitoring programs.
Earlier this year, the Obama administration said it would begin working on new regulations to cap mercury emissions from power plants.
Mercury is a neurotoxin and is considered to be one of the most serious contaminants threatening the nation's waters. Pregnant women are specifically advised to avoid mercury consumption because of its potentially damaging effects on the brains of fetuses.
The Associated Press contributed to this report.
- Link: U.S. Geological Survey