San Joaquin River is No. 2 on national ‘endangered’ list

The San Joaquin River and its three main tributaries ranked second on a list of “endangered” streams released by a national group.

Water demand from farms and cities has sapped the San Joaquin, Stanislaus, Tuolumne and Merced rivers, says the annual report from American Rivers, based in Washington, D.C.

“Dams, levees and excessive water diversions have hurt river habitat and opportunities for recreation and community access,” says the report released Tuesday. “The river’s salmon and steelhead populations are on the brink of extinction.”

American Rivers called on the State Water Resources Control Board to boost the flows. That agency already has proposed that they increase to 35 percent of natural conditions from February through June of each year – something water users say would mean lost food production and jobs.

It’s not the first time the San Joaquin River system has appeared on the endangered rivers list. It ranked No. 1 in 2014, and in 2009 it topped the list in conjunction with the Sacramento River system. American Rivers compiles the list annually to draw attention to current or pending threats it sees on the streams, including dams, hydroelectric plants, mining and pollution. Ahead of the San Joaquin River on the 2016 list at No. 1 is the Apalachicola/Chattahoochee/Flint river system in Georgia, Alabama and Florida.

In its assessment of the San Joaquin, the American Rivers report declares that the primary threats are outdated water management and excessive diversions from the river’s natural flow.

“Years of managing the San Joaquin for agriculture, hydropower and flood control have taken their toll on the river,” the report states.

“The river is so overtapped that in some places it runs completely dry, threatening water quality, endangering fish and wildlife, creating uncertainty for farmers, and leaving communities vulnerable in the face of more frequent and severe droughts,” the report says.

The river is a focus of a major restoration project that includes state and federal water agencies as well as irrigation districts, environmental organizations and nonprofits up and down the length of the river from Fresno to the San Joaquin-Sacramento River Delta. American Rivers is one member of San Joaquin River Partners, a coalition of environmental groups that includes Fresno’s San Joaquin River Parkway and Conservation Trust.

Steve Ottemoeller, water resources manager for the Friant Water Authority, said he doubts whether the American Rivers designation will have any practical effect.

“I don’t think it will make anything happen sooner” for the restoration efforts, he said. “Things are already in play to make the improvements that these folks want to make.”

The Friant Water Authority, which represents irrigation agencies on the east side of the San Joaquin Valley that receive river water from the Madera Canal and the Friant-Kern Canal, is among the numerous signatories to a complex legal settlement over the river restoration.

“I was a little surprised when (the river) was named No. 1 a couple of years ago because we’re in the process of working on the restoration,” Ottemoeller added. “That was something that was negotiated and signed by the courts in 2006. … It’s an ongoing activity, and we would expect it to continue to get better.”

The state board is expected to announce a revised proposal this year for the February-to-June flows on all four rivers. The aim is to improve fish numbers and water quality there and downstream in the Sacramento-San Joaquin Delta.

One major goal of the river program is restoration of a viable salmon fishery on the San Joaquin. Farmers who rely on the river for irrigation, however, say that may be an unrealistic expectation so many years after the construction of Friant Dam in the late 1930s and early 1940s dramatically changed the character of the river on the Valley floor.

Kole Upton, a farmer in the Chowchilla area and a board member of the farm-advocacy group Families Protecting the Valley, said the river and its users face a “challenging situation” posed by restoration efforts, drought and climate change. A long-term trend of warming, he said, is rendering the river – which he described as “the southernmost periphery of salmon viability” – as an area where the water is too warm for salmon to survive, much less thrive.

“But environmental ideologues are bound and determined that we’re going to do this restoration, no matter what,” he added.

Instead of the cold water needed by salmon, Upton is among advocates for a warm-water fishery on the San Joaquin, which he called a “common-sense solution” that restores water flow to the river without shutting down deliveries of surface water for agriculture.

“We need a good, healthy environment, and we need fisheries,” he said, “but we can’t do it in a manner that jeopardizes the livelihoods and the communities that rely on agriculture.”

Michael Martin of Mariposa, director of the Merced River Conservation Committee, urged steps aimed at enhancing agriculture and the ecosystem. They include water efficiency on farms and “conjunctive use” of rivers and groundwater.

“Science has found that a healthy river needs more water,” Martin said. “We have to work together to find solutions to better manage the water we have.”

But even Upton acknowledged that environmental groups are unlikely to budge from the idea of restoring salmon runs. And proposals for a new dam at Temperance Flat above Millerton Lake to store more San Joaquin River water for dry years seems to run counter to American Rivers’ aspirations.

Indeed, American Rivers is urging supporters to lobby the State Water Resources Control Board “to increase the water flows in the San Joaquin to keep it healthy.”

“California’s ongoing drought places additional stress on the river and its communities, but we must not allow the drought to force rash decisions – such as cutting environmental protections or building expensive new dams at taxpayer expense – that will harm the river, fish, wildlife and communities for years to come,” the report states.

Upton said depriving agriculture of surface water from the river, however, is counterproductive to the health of Valley communities and farms that must rely on water pumped from the ground when water allocations are cut.

“We need groundwater restoration to save the aquifers; that’s something that has to be done. We cannot keep going overpumping the ground water,” Upton said. “But this isn’t going to work if the state and federal agencies keep taking surface water away.”

This story was originally published April 13, 2016 at 8:36 AM with the headline "San Joaquin River is No. 2 on national ‘endangered’ list."