The Merced River is not often thought of as ground zero in the state's water wars.
Most think of it as just one of many dammed-up rivers that make their way from the Sierra to the Valley floor and feed the San Joaquin River's path north.
But because of the overuse of the San Joaquin River water south of Merced County, the Merced River has effectively become the San Joaquin's headwaters, according to water managers and environmentalists.
So the re-licensing of Merced Irrigation District's dams on the Merced River with the Federal Energy Regulatory Commission may have much farther reaching consequences in a state water system of interconnected mazes of pumping stations and canals.
"The Merced is essentially the headwaters of the San Joaquin River," said Ron Stork, a senior policy advocate at Friends of the River, an environmental group.
Three rivers, the Merced, Tuolumne and Stanislaus -- the Merced being the first and furthest south -- are all that contribute to the San Joaquin's meager northward flow.
Much of that water, along with water from the Sacramento River, is pumped back south to Westside farmers and Southern California's cities through the Delta Mendota Canal and the California Aqueduct, according to state and federal officials.
So much water is diverted from the Central Valley Water Project's Friant Dam in Fresno County that the San Joaquin River is little more than a stream for much of its southern length, Stork said.
"The San Joaquin is kind of a stagnant, very turbid, river," he said.
By the time it crosses Highway 99 and heads north, the river is all but gone. It only becomes a real river again where it meets the Merced River.
Currently, the Merced and its two sister rivers to the north, the Tuolumne and Stanislaus, make up the the San Joaquin's main watershed, according to the irrigation districts and federal managers of dams along those rivers.
Each year, the three rivers main dams must release a certain amount of water to the San Joaquin depending on drought conditions and federal environmental regulations.
The Merced River releases 159,000 acre-feet in a normal year (An acre foot is equivalent to 326,000 gallons.)
Upstream the Tuolumne's Don Pedro Dam, run by Turlock Irrigation District and Modesto Irrigation Canal, released 158,386 acre-feet into the San Joaquin in 2008. Finally, the Stanislaus River's New Melones Dam, run by the Bureau of Reclamation, releases more than 800,000 acre-feet a year.
These combined releases make up the majority of San Joaquin water that flows into the delta.
Not far from the mouth of the San Joaquin, north of Tracy, is the California State Water Project's pumping station.
In 2008, according to the California Department of Water Resources, 1,633,324 acre-feet were pumped from the delta at this site, the majority of which went to Southern California.
The Bureau of Reclamation has its own pumping station nearby -- part of the Central Valley Water Project -- which in turn pumps roughly 2 million acre-feet a year south along the Delta Mendota Canal, according to the bureau.
While the pumping from the delta by these two bodies is dependent upon a series of factors -- tides, rainfall and snowmelt -- there is no way to count water molecules, said Stork, so it's unknown where the water that is taken south actually comes from -- the Sacramento or the San Joaquin River.
For instance, in a wet year the state puts 85 percent of the Feather River's flows into the Sacramento and hence the delta. But the delta pumps are closer to the San Joaquin than the Sacramento where the Feather's water ends up.
Much the same is true for the Bureau of Reclamation's CVWP.
Two huge northern dams -- Shasta and the Keswick -- release 5.1 million acre-feet into the Sacramento River every year. (Friant Dam on the San Joaquin is also run by the CVWP.) But the project's pumping station -- like the state's -- is closer to the mouth of the San Joaquin than the Sacramento where most of the CVWP's water flows into the delta.
Pete Lucero, the Bureau of Reclamation's spokesman, says that it's not that simple. The San Joaquin might be closer to the pumps, he said, but the sheer volume of water coming into the delta does not compare to the much larger Sacramento.
"The Merced River is not a major factor in the CVWP," said Lucero. Neither are the other rivers that flow into the San Joaquin.
While the Merced River's contribution to the state's water picture is small compared to the whole, a change in its FERC licensing could affect its down-river flows.
The licensing process, that will end in 2012, is moving toward a scoping document that will effectively study the area influenced by the river's dams. That scoping document is a bone of contention between the river's stake holders.
PG&E and MID, that own dams on the river, want the study of the dam's effects to be limited to the immediate environs of Lake McClure. Environmentalists want the study to go as far as the delta.
Whichever side's choice is picked may influence the rules under a new license, specifically water releases.
Whatever happens on the Merced will influence decision that affect delta fish, nearby dams, Westside farmers and Southern Californians.
Reporter Jonah Owen Lamb can be reached at (209) 385-2484 or firstname.lastname@example.org.