FRESNO -- An intense fight is emerging on the valley's west side between farmers and activists who seem to have the same goal -- protecting the San Joaquin River.
Activists say toxic irrigation drainage from the farms could undermine river restoration by poisoning newly restored salmon in 2013, when federal authorities are scheduled to begin the fish runs.
Farmers, who have been voluntarily cleaning up the drainage since 1995, say the fish will be fine, because high restoration flows will dilute possible contaminants.
An emotional debate is expected before the State Water Resources Control Board, which will decide how much time farmers have left to eliminate the bad water. No date has been set, but the board probably will consider it before the end of the year.
At issue for farmers is a 97,000-acre swath of land between Interstate 5 and Firebaugh. Farmers came up with the drainage cleanup -- called the Grassland Bypass Project -- because they knew authorities eventually would require them to protect the river or face some form of land retirement.
The river restoration will enter its second year this fall, as officials continue sending test flows down the waterway from Friant Dam. Two long dry stretches of the river have been refilled, and the San Joaquin has been reconnected with the Pacific Ocean.
That sets the stage for the next step in the project -- reintroduction of salmon runs.
Selenium, a natural element in the west-side soil, is a big concern for the restored salmon runs, say activists. Selenium is essential for life, but in high concentrations, it will kill or cause deformities in animals.
Irrigation drainage collects selenium in high concentrations. The river also gets big doses of selenium during storms, when uncontrolled runoff drains into the San Joaquin.
Before the mid-1990s, the irrigation drainage passed through sensitive wetlands on its way to the river, damaging the ecosystem. For the past 15 years, farmers have protected the wetlands by capturing the drainage and sending it to the river through a concrete canal and a slough.
In the process, farmers have cut down on the amount of drainage water by installing stingy drip irrigation and recycling drain water. They've spent $100 million, about half of which was government funding, and much of the selenium and salt contamination has been wiped out.
But activists say the cleanup has not progressed far enough to protect salmon. They found a federal research biologist who agrees, and they will cite his opinion in their arguments.
The statewide activist groups trying to protect the restoration from the farm drainage include the California Sport Fishing Alliance and the California Water Impact Network.
"The drainage contaminants accumulate in the system," said Tom Stokely of the impact network. "They don't break down into something harmless."
Activists suggest farmers be given two years for the drainage cleanup, saying they already have missed a deadline last year for meeting the water-quality standards. They say the project's tainted water in a five-mile stretch from Mud Slough to the confluence of the Merced River will create a toxic gauntlet that restored salmon must run if the cleanup takes longer.
But farm officials in the last year have gotten the green light for an extension to 2019 from the U.S. Bureau of Reclamation and one state watchdog, the Central Valley Regional Water Quality Control Board.
Farmers say they need the extra time to develop a treatment plant to eliminate the rest of the bad water. They must submit a plan on the treatment plant by 2013 and reduce selenium levels by 40 percent from the current levels over the next five years.
Farm officials say their studies show that increased freshwater during salmon migration will dilute contamination and move it out, especially during the higher flows that the restoration must have to help the salmon move.
The Bureau of Reclamation, supervising the Grassland project, agreed after looking at additional studies from the U.S. Fish and Wildlife Service, which raised some concerns about the drainage. Bureau officials are aware of the concerns, but they said the bypass project is a key river improvement.
An oversight committee has been appointed to investigate any fish or ecosystem problems and require adjustments in the bypass project if needed, officials said.
The committee consists of the Bureau of Reclamation, U.S. Fish and Wildlife Service, U.S. Environmental Protection Agency, California Department of Fish and Game, and the Regional Water Quality Control Board. If there are problems, the committee can adjust the project to protect the river.