However, the agency said oil-related materials from motor vehicles and shipping continue to enter coastal waters.
The overall improvement was credited to environmental laws enacted in the 1970s.
Gunnar Lauenstein, manager of the NOAA's Mussel Watch program, said: "It's interesting to note that pesticides, such as DDT, and industrial chemicals, such as PCBs, show significant decreasing trends around the nation, but similar trends were not found for trace metals."
The report is based on a study by Mussel Watch covering coastal areas from 1986 to 2005.
--Levels of DDT were down nationally, particularly along the Southern California coast.
--There was a decrease in PCBs. The Hudson-Raritan Estuary, an area where some of the highest concentrations of these chemicals were found, now shows 80 percent of monitored sites with significantly decreasing trends.
--The biocide tributyl-tin, used to reduce marine organisms on boat hulls, was found to affect other marine and fresh water life as well. First regulated in the 1980s, this compound is now decreasing nationally.
--Oil related compounds from motor vehicles and shipping activities continue to flow into coastal waters daily.
--Flame retardants known as PBDEs are a new class of contaminants and are being evaluated to determine whether they are increasing in coastal waters and what effects they may have on both marine and human health. The agency plans to issue a report on flame retardants in coastal waters later this year.