The Laguna de Santa Rosa and Russian River have unacceptable levels of mercury and other pollutants, according to a preliminary study released by the state.
In addition to the river and laguna, the draft list of area bodies of water that do not meet federal Water Quality Act standards includes Bodega Harbor, the Mendocino Coast, Noyo River, Big Sulphur Creek, Santa Rosa Creek, Albion River and the Klamath River.
Pollutants found include mercury, sediment, silt and high water temperature.
But state water officials acknowledged that some new listings may have occurred because more data is available than when previous reports were compiled, not because water conditions have worsened.
In addition, the removal of a number of waterways from the pollution list might have occured because of a lack of information, not because water quality has improved.
"Every year, it becomes possible to collect more data, so the reasons that bodies of water may be added to the list is simply that the data wasn't collected (in past studies)," said William L. Rukeyser, spokesman for the State Water Resources Control Board, the agency that conducted the study.
"We are at a preliminary phase," he said.
The release of the study, the first since 2002, opens a 60-day public comment period that will culminate with two public hearings in December. The state is then expected to amend the list and submit it to the Environmental Protection Agency for compliance with the Clean Water Act.
Findings are expected to be made final in 2006. Plans for fixing any problems - including restricting certain uses and fining violators - are created once the list is finalized.
Despite the presence of pollutants, the levels found do not justify concern over the safety of area drinking water, analysts said.
"Drinking water uses are some of the less vulnerable uses," said Dave Smith, a team leader with the EPA. "Of course, any mercury is too much. It's a real potent neurotoxin."
Between 1996 and 2000, three out of 17 samples in the laguna and Russian River sample area showed unacceptable levels of mercury in fish.
"We are being prudently cautious," Rukeyser said.
While the presence of mercury is troubling, local water officials also expressed concern over the state's de-listing of some local waterways.
Turbidity - or cloudy water filled with sediment - and nitrogen and phosphorous are now at acceptable levels in the Russian River, according to the latest study. The laguna also was dropped from the list of unacceptable levels of nitrogen and phosphorous.
"There is a lot to be desired in the amount of information we have seen," said Bruce Gwynne, environmental scientist with the state North Coast Water Quality Control Board.
Unlike in years past, state officials based in Sacramento conducted the bulk of the study, rather than tapping local officials to investigate, Gwynne said.
The result, he said, is a report based more on "data-driven measures than professional judgement."
The final list is likely to change before being accepted by the feds, Gwynne said.
The draft proposal is posted on the state agency's Web site at www.waterboards.ca.gov/tmdl. The public has 60 days to comment on the report before it is amended and forwarded to the EPA.
All comments must be submitted by Dec. 6. Two public hearings are scheduled, including one in Sacramento on Dec. 6 at the State Water Board's Sierra Room.