By Alex Breitler

Record Staff Writer

April 10, 2014 12:00 AM

San Joaquin County’s namesake river has been named the most endangered stream in America by an environmental group.

The concerns raised by Washington, D.C.-based American Rivers are not new. The San Joaquin routinely runs dry upstream of Stockton because of water diversions to San Joaquin Valley farmers, and closer to Stockton the river carries large amounts of polluted runoff from farms.

But John Cain, the group’s California conservation director, said Wednesday that the San Joaquin seems to be at a “tipping point.”

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The most endangered rivers in the U.S., as determined by the environmental group American Rivers:

1) San Joaquin River

2) Upper Colorado River

3) Middle Mississippi River

4) Gila River (New Mexico)

5) San Francisquito Creek (Bay Area)

6) South Fork Edisto River (South Carolina)

7) White River (Colorado)

8) White River (Washington)

9) Haw River (North Carolina)

10) Clearwater/Lochsa rivers (Idaho)

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First, state officials are embarking on an effort to determine how much water should be allowed to flow down the San Joaquin and its tributaries in future years – a “long overdue” process for which American Rivers is attempting to muster support.

Second, Valley Republicans have been attempting to overturn a settlement agreement to restore the dry stretches of the river and bring back long-dead salmon runs. Wednesday’s report attempts to ward off those efforts and urges officials to move forward with the restoration plan.

“We speak for the river,” Cain said. “If we don’t speak for the river, who else will?”

It’s not the first time a local stream has shown up on American Rivers’ annual list. While not a river, per se, the Delta as a whole was listed as the most endangered “river” in the country in 2009, and showed up again on the list in 2010, that time ranking No. 2.

The San Joaquin restoration project, launched in 2006, is taking longer than expected and has gotten more expensive. Originally pegged at $250 million to $800 million, the cost as of summer 2012 was estimated at $892 million.

Before the drought, officials did begin releasing water downstream to test the channel, and they reintroduced some salmon as an experiment to see how a fully functioning salmon run might fare in the stream.

But physical improvements that will be needed within the river channel have not yet been constructed. And for the moment, the drought has made any additional restoration flows impossible.

Cannon Michael, who farms along the river near Los Banos, acknowledged the long-standing problems for the San Joaquin but questioned whether the restoration project – which he said seems to be the driving force behind the river’s dubious ranking – remains plausible.

“A lot of things have happened, and it’s not the program’s fault,” Michael said. “I just wish there could be a more realistic discussion about it, because the truth is it is facing some enormous challenges.”

Contact reporter Alex Breitler at (209) 546-8295 or abreitler@recordnet.com. Follow him at www.recordnet.com/breitlerblog and on Twitter @alexbreitler.