The South Carolina Sierra Club Water Committee said 31 percent of the rivers in 2006 had bacteria counts too high for bodily contact. That was up from 19 percent two years earlier.
Officials with the state Department of Health and Environmental Control say they have been working on the problem for years.
"We absolutely feel like we're making progress on impaired waterways," said Adam Myrick, a spokesman for the agency.
The primary pollutant is fecal coliform bacteria - which comes from human and animal waste and gets into waterways as the result of storm water runoff, faulty septic systems, farm animals using streams, and sediment from farms and grazing areas.
Of 1,972 water sites monitored by the state, 915 were rated as impaired by the agency during monitoring from 2000 to 2004, the most recent figures available, Mr. Myrick said.
Although many streams have severe problems, the Savannah River isn't prone to fecal coliform issues, said Frank Carl, the director of Savannah Riverkeeper Inc., an environmental group.
"There isn't much of a fecal coliform problem on the Savannah, mainly because there is so much water," he said.
"Fecal coliform is mainly from sewer spills or septic tanks, and there aren't too many houses close to the river with septic tanks."
At least four South Carolina streams in the Savannah Ricer drainage basin have been identified as having such problems, according to the U.S. Environmental Protection Agency. They include Eighteen Mile Creek, Twenty Mile Creek, Little River and Long Cane Creek, all in McCormick, Abbeville, Anderson and Greenwood counties.
Staff Writer Rob Pavey and The Greenville News contributed to this report.