http://www.digitaljournal.com/news/environment/california-s-san-joaquin-river-agriculture-vs-a-healthy-river/article/477934

California's San Joaquin River — agriculture vs. a healthy river

Posted Oct 23, 2016 by Karen Graham
The San Joaquin River is the longest river in Central California, and the second most endangered river in the country. But because of dams, levees, and water diversion, over 100 miles of the river has been dry for 50 years.
FISH: Mature chinook salmon swim upstream in the Lower Tuolumne River in California s Central Valley...
FISH: Mature chinook salmon swim upstream in the Lower Tuolumne River in California's Central Valley in 2008.
Dan Cook USFWS/Wikimedia Commons
The San Joaquin River is second only to the Apalachicola, Chattahoochee and Flint rivers basin in Alabama, Georgia, and Florida as a seriously endangered river in this country.
The San Joaquin River, along with its three main tributaries, the Stanislaus, Tuolumne and Merced rivers, have been so sapped of water over the years that it has affected more than 70 percent of their natural flow., according to an annual report from American Rivers, based in Washington D.C.
Dry irrigation channel of the San Joaquin River.
Dry irrigation channel of the San Joaquin River.
Alison M. Jones/American Rivers
The report called on the State Water Resources Control Board to boost the flow of the river, but the state agency had already proposed boosting flow by 35 percent from February through June of each year, a recommendation that was not well received by farmers.
Now, the U.S. Bureau of Reclamation says that by the end of this month, a 150-mile stretch of the river will again have water flowing through it for the first time in 50 years. The purpose of doing this is to allow salmon to again swim up to the Sierra Nevada foothills to spawn, reports ABC News.
The headwaters of the San Joaquin River start as snowmelt in the high reaches of the Sierra Nevada M...
The headwaters of the San Joaquin River start as snowmelt in the high reaches of the Sierra Nevada Mountains.
Hike395
But the circumstances and problems surrounding the San Joaquin River and its status are very complicated, and there are no easy solutions. We have to acknowledge that California is in its fifth year of an ongoing drought, and coupled with diversions of water for years on end has made any solution a tricky proposition.
The report states: "The river’s salmon and steelhead populations are on the brink of extinction. Excessive diversions, groundwater overdraft, and poorly designed levees have left the river and surrounding communities vulnerable to increasingly frequent and severe droughts and floods."
As a keystone fish species, the salmon are important to the environment, besides being a prime fish for fishermen. The salmon used to be able to migrate up the river to spawn and die, their bodies decomposing and adding nutrients to the soil, making the Central Valley a major agricultural region.
An example of heavily irrigated farmland in the northern San Joaquin Valley  near Tracy and Manteca.
An example of heavily irrigated farmland in the northern San Joaquin Valley, near Tracy and Manteca.
Coolcaesar.
The 366-mile long San Joaquin river is the most dammed river in the state, beginning as snowmelt in the high Sierra Nevadas and flowing down through granite canyons until it reaches a reservoir at Friant Dam east of Fresno. From there, it is a dry river bed for much of the year. Further down, near Mendota, it picks up again, but only with the help of several tributaries before feeding into San Francisco Bay.
When the Friant reservoir was constructed in 1949, it did two things. It halted the yearly salmon runs up the river and gave farmers access to more water, increasing agricultural production in the region. Then in 1988, the Natural Resources Defense Council decided to restore the river, and the battle was on.
Millerton Lake  the reservoir of Friant Dam and the largest on the San Joaquin mainstem.
Millerton Lake, the reservoir of Friant Dam and the largest on the San Joaquin mainstem.
Kjkolb
In a 2006 settlement that supposedly ended the battle, farmers had to agree to give up 18 percent of the water in the Friant dam. That's when a movement began to bring back the salmon by 2012.
"It was a longshot, to say the least, that everything would be executed on that timeline," said Jason Phillips, who led early efforts by the U.S. Bureau of Reclamation to restore the river.
Now a CEO of the Friant Water Authority, Phillips says he calls it "an open question" whether the river can be revived as the project envisions. He cites two reasons why he feels this way. One is that water has become even scarcer since regulations were put into effect, and two, he says that climate change wasn't calculated into the original plans.
But added to the complexity of the problem is something we all know about, money, or the lack of money. What was to be an $800 million project has ballooned into a $1.7 billion elephant of a project. So we will wait and see.