By Ian Simpson

WASHINGTON (Reuters) - Fifty-five percent of U.S. river and stream lengths were in poor condition for aquatic life, largely under threat from runoff contaminated by fertilizers, the U.S. Environmental Protection Agency said on Tuesday.

High levels of phosphorus and nitrogen, runoff from urban areas, shrinking ground cover and pollution from mercury and bacteria were putting the 1.2 million miles (1.9 million km) of streams and rivers surveyed under stress, the EPA said.

"This new science shows that America's streams and rivers are under significant pressure," Nancy Stone, acting administrator of the EPA's Office of Water, said in a statement.

Twenty-one percent of the United States' river and stream length was in good biological condition, down from 27 percent in 2004, according to the survey, carried out in 2008 and 2009 at almost 2,000 sites.

Twenty-three percent was in fair condition and 55 percent was in poor condition, the survey showed. The finding uses an index that combines measures for aquatic life, such as crayfish and water insects.

Of the three major climatic regions surveyed - eastern highlands, plains and lowlands, and the west - the west was in the best shape, with 42 percent of stream and river length in good condition.

In the eastern highlands and the plains and lowlands, 17 percent and 16 percent of waterway length respectively was in good condition.

By far the most widespread stress factor was phosphorus and nitrogen, which are used in fertilizer. Forty percent of river and stream length had high levels of phosphorus and 28 percent had high levels of nitrogen, the report said.

Risk levels of mercury in fish tissue were exceeded in 13,144 miles of rivers. Streams were not surveyed. In 9 percent of river and stream length, samples for enterococci bacteria topped levels for protecting human health.

Federal, state and tribal researchers carried out the survey at sites ranging from the Mississippi River to mountain streams.

The survey report is the first statistically based overview of the condition of U.S. rivers and streams.

(Reporting by Ian Simpson; Editing by Daniel Trotta and Steve Orlofsky)