Water once again flowing in the San Joaquin River

The San Joaquin River was once big enough to carry steamboat-loads of passengers from the north to a booming Fresno. The lush banks and its gentle water provided relief on hot summer days. In the water, a plentiful run of Chinook salmon traveled hundreds of miles from the Pacific Ocean to breed at the southernmost salmon run in North America.

"Historically, the salmon populations on the San Joaquin River numbered in the hundreds of thousands," Natural Resources Defense Council spokesperson Monty Schmitt said.

But there are no salmon there anymore. In fact, until this spring, long stretches of the San Joaquin River had been wiped out, cut off from the water that once flowed past its swollen banks.

The Friant Dam was the plug that stopped the San Joaquin. It was completed in the 1940s to provide water for the farms that sprang up on the fertile soil of the Central Valley and flood protection for the towns downstream.

"And by 1945, canals that take water from Friant Dam were completed, and that's really when parts of the San Joaquin River began to dry up," Schmitt said.

Schmitt is one of a number of scientists and environmentalists who say life may soon return to the dead San Joaquin River.

The NRDC filed suit against the Bureau of Reclamation in 1988, demanding the water flow again and the salmon be brought back.

Sixteen years later a federal judge ruled the bureau had violated state law by not providing enough water to sustain the fishery downstream.

In 2006, a settlement agreement had been reached between the feds, the state, water users and environmentalists.

"The benefit of the settlement agreement, while nobody getting everything they wanted, it was something we could all live with and work towards and agree upon," Schmitt said.

This March, NRDC cameras captured San Joaquin River water flowing from the Sierra to the Sacramento Delta for the first time in more than half a century, opening the floodgate on the largest river restoration project in U.S. history.

"The next 15 years we will begin and have begun making releases from Friant into the river," Bureau of Reclamation spokesperson Jason Phillips said.

Philips is the program manager for the San Joaquin River restoration program. It is expected to cost $250-$850 million to restore it.

"The channel improvements include, in some areas, setting back levees substantially beyond the banks of the river to allow for overflow," Phillips said.

New bypasses will need to be built to let fish pass dams; where the river has been blocked will need to be restored or re-routed; and salmon breeding habitat will have to be restored for their reintroduction.

"The goal is to have a naturally reproducing, self sustaining population of Chinook salmon -- spring and fall run -- and the settlement also calls for other native fish," Calif. Department of Fish and Game spokesperson Gerald Halter said.

A new salmon hatchery will go in downstream from the Friant Dam in order to make that happen.

But all these changes will not come without a cost to Central Valley water users.

"It will reduce the amount of water delivered to the Friant water users by about 15 percent," Phillips said.

"Some of our districts are totally dependent on Friant supplies," Ron Jacobsma of the Friant Water Users Authority said.

The Friant Water Users Authority represents the users of San Joaquin River water. Many are farmers and ranchers. Under the settlement agreement, those customers will likely be fine in average years, but it is the dry years that will be the true test of the settlement's viability.

"A lot of our plantings are permanent; you can't really shut a citrus tree off or grapes or nut trees off for just a single year, if you lose them for a year you've lost five or six years of investment just to get them to produce a crop," Jacobsma said.

Farmer Kole Upton was among the settlement negotiators. Under the agreement, water taken away to flood the San Joaquin could be replaced with other sources, including water from the Sacramento Delta. Upton worries the future of that supply; environmentalists are now in court raising concerns about the salmon habitat there and the future of the delta smelt.

"I thought that the money we'd save would enhance the other fisheries that are in such bad shape; rather than try to start a dead river and bring 500 fish up, why don't we try to work on the Eel, the Merced, the Stanislaus that already have an existing salmon run and invest in that?" Upton said.

But environmentalist and scientists say the salmon will eventually come back and they do not have to look any farther than where the water flows again to see that life is slowly returning to the San Joaquin River.

Under the current settlement agreement there will be a series of milestones that will have to be reached. In 2026, all parties will come back to the table and assess where things stand.

Written and produced by Ken Miguel

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