This ruling by U.S. District Judge William Alsup allows federal regulators to combat such pollution by pressuring states to change land-use practices.
Federal officials, including EPA Administrator Carol M. Browner, said they hope the ruling starts a national trend.
This important decision allows us to build on our success of completing the task of cleaning our nation's waters," said Browner.
The ruling concerns provision of the 1972 Clean Water Act that EPA did not start to enforce until 1991 under pressure from courts and environmental groups.
The provision allows the agency to tell states to come up with ways to reduce pollution in rivers and waterways contaminated solely by runoff, as opposed to industrial waste or sewage.
EPA says runoff has become the leading threat to water quality in the United States.
The agency was sued by two California landowners, the American Farm Bureau Federation and state and local farm organizations.
The court heard a challenge to an EPA decision to put the Garcia River on the list of impaired waterways in California and define the amount of sediment that should be allowed to enter the river from land along its banks.
EPA said the river's coho salmon and steelhead populations have been severely damaged by sediment from many years of logging.
In March 1998, EPA developed a "total maximum daily load" (TMDL) for sediment for the river.
A TMDL defines the greatest amount of a particular pollutant that can be introduced into a waterway without exceeding the river's water quality standard.
The agency also defined the reductions in sediment that are necessary for the river to attain the water quality standard set by the State of California.
The American Farm Bureau Federation and other agriculture and timber groups said that EPA and the states should calculate TMDLs only for pollutants that are discharged from pipes, or point sources.
The court disagreed, ruling that the Clean Water Act is designed to provide a comprehensive solution to the nation's water quality problems, "without regard to the sources of pollution."
In California, only 1 percent of impaired waterways fail to meet water quality standards solely because of pollution that comes from pipes, municipal waste treatment works, or other point sources.
According to EPA, 54 percent of California's impaired waterways are polluted by nonpoint sources exclusively, while another 45 percent are impaired by a combination of point and nonpoint sources.