San Joaquin River battle far from over in Central Valley

Steve Chedester, executive director of the San Joaquin River Water Authority, shows where four gates stop and then redirect the flow of the San Joaquin River northwest of Los Banos into the Eastside Bypass, to the left of photo.
Steve Chedester, executive director of the San Joaquin River Water Authority, shows where four gates stop and then redirect the flow of the San Joaquin River northwest of Los Banos into the Eastside Bypass, to the left of photo. File photo

The revival of the San Joaquin River will officially begin with a shot of fresh water in October -- capping decades of courtroom battles and years of delicate negotiations over funding.

But the wrangling over the state's second-longest river is far from over.

People are only now beginning to discuss other issues, such a proposal by developers in Madera County to pour treated sewage into the river not far from salmon-spawning areas.

Some people also are wondering how to keep downstream water users from siphoning the restoration water. And east-side farmers, who will give up irrigation water for the restoration, want authorities to recapture and return some water to farm fields.

Meanwhile, a lot of people are ready to argue about the exact course of the rebuilt river.

Congress soon is expected to give the green light to $88 million in restoration funding for a settlement in the river lawsuit, which was filed nearly 21 years ago to restore salmon to the river. The full restoration price tag could eventually be 10 times higher.

The restoration would make the river a continuous stream again, connecting a fractured, 153-mile stretch from Friant Dam to the mouth of the Merced River. Beyond the Merced the river has remained a flowing stream to the Sacramento-San Joaquin River Delta.

With the first revival flows coming this fall, local activists say it's time to consider the river differently.

"It will become a statewide drinking water source. It will become habitat for endangered species and migratory fish," said Chris Acree, executive director of Fresno-based Revive the San Joaquin. "It will become a new recreational source." A lot more people along this 350-mile river will pay closer attention now. Some already have a major criticism of the river restoration: Only a handful of government agencies are directly involved in the planning.

The five state and federal agencies, led by the U.S. Bureau of Reclamation, provide monthly reports available on the Web. But most people will have to get the real details from thick, environmental documents that will be released later this year.

The interested groups range from landowners near Friant Dam to water agencies more than 150 river miles downstream on the Merced, Stanislaus and Tuolumne rivers. They are so-called third parties, but they say they are directly affected.

One such group, represented by the San Joaquin River Exchange Contractors Authority, includes landowners whose property could be altered drastically in the restoration. The landowners plan to hire engineering consultants to check the government's work, officials said.

"Either you trust the government, or you don't," said authority executive director Steve Chedester. "And we don't. The landowners want to confirm or to verify the plans and, if need be, dispute them." Bureau of Reclamation officials say plans for this project -- the West's largest river restoration -- are coming together as quickly as possible. Officials are separately considering many different stretches of the restoration.

One important stretch is northeast of Dos Palos. It is little more than a withered slough. During big snowmelt years when huge amounts of water pour out of the mountains, the river's water has been sent through a parallel channel called the Eastside Bypass.

Should the restored river go through the bypass, or should federal officials dig a channel along the old river course? Area landowners say they don't think public money should be used to rebuild the old channel when the massive bypass is already built.

The decision will be made as the environmental documentation is completed, said Jason Phillips, bureau project manager based in Sacramento. The bureau's timeline shows any extensive work on that part of the channel would take place in early 2012.

Phillips said this year's release of water -- called an interim flow -- will teach officials a lot about the river channel. Nobody knows how much water the dried river bed will absorb.

"There are hypotheses, but we don't have the data we need yet," he said.

By Dec. 31, 2012, salmon are supposed to be re-introduced into the river. At that point, the river is supposed to be a continuous stream from Friant Dam to the delta.

Fresno-area activists are afraid the river will some day carry water tainted with treated sewage from proposed developments near the river.

Acree of Revive the San Joaquin said his group is a party to a lawsuit against Madera County, which already has approved two developments, the Northshore at Millerton and Tesoro Viejo.

The developers of the two projects would build 8,200 homes along Highway 41 near Millerton Lake. The projects are part of the Rio Mesa area that some day could be home to 100,000 residents.

Acree said the developers need to provide a plan to deal with the treated waste water without flushing it into the river.

"They didn't even give lip service to the river restoration in the EIR," said Acree. "It's like the plan to restore an endangered species does not exist." Madera County officials, who approved the developments, defend the projects, saying they meet tough environmental state standards.

Downstream, the restoration-channel work ends where the Merced River meets the San Joaquin, but possible conflicts continue for another 118 miles to the delta. Farms, cities and industries use the river as it passes through the rest of the Valley.

Many have rights to water from the San Joaquin River, but no one has talked much about the fate of the restoration water once it passes the mouth of the Merced River.