By Lisa Lambert

WASHINGTON, June 5 (Reuters) - More than one-third of the coastal waters that link America's rivers and oceans are in poor condition, the Environmental Protection Agency said in a report on Tuesday, with Puerto Rico and the Northeast coast faring the worst.

The EPA analyzed 1,239 sites in its first survey of the country's 28 major estuaries, which provide breeding grounds and shelter for fish and birds.

It found that bodies of water with large numbers of people living nearby suffered the most. While counties with big estuaries make up only 6 percent of the coastal land area, they contain more than two-thirds of the coastal population.

The impact of building communities and shipping facilities, and providing them with sewers, put the estuaries under stress.

In estuaries in Northeastern states, between 10 and 20 percent of the water was polluted, and more than 15 percent of the sediment was contaminated, the survey found. More than 10 percent of the organisms and fish in the estuaries facing the northern Atlantic Ocean suffered from chemical contamination.

Estuaries in the Southeastern states were in the best condition, the report said. Less than 10 percent of the water was polluted and about 5 percent of the sediment showed signs of toxins.

The survey also found that the entire San Juan Bay Estuary in Puerto Rico was in poor condition.

Estuaries provide more than 75 percent of the U.S. commercial fish catch, according to the EPA, and the fisheries are worth more than $1.9 billion.

The EPA said estuary administrators should work with local officials to develop stormwater management plans to curb the contaminated water that runs off into the estuaries.

Rob Brumbaugh of the Nature Conservancy said the EPA's report was a call to action.

"The one thing we know is that estuaries, although they are threatened, they are pretty resilient and respond to restorations," Brumbaugh said. "The mixture of the fresh water input and the saltwater creates ecosystems that are used to fluctuations."

He said the report helped identify estuaries that are thriving and need to be shielded from development as well as those that need rebuilding.

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