The first phase of the State Water Board’s process for an updated water quality control plan (planned for completion in early 2013) will be a determination of flow objectives for the lower San Joaquin River to protect fish and wildlife and salinity objec- tives for the southern Delta to protect agriculture in the area. Advocates for increased flows on the river say they are an important part of restoring the Delta and the aquatic ecosystems of the larger Central Valley watershed. “For decades, the vast majority of the fresh water runoff in the San Joaquin Valley has been diverted before it reached the Delta – in some recent years, almost 90 percent of the flow never made it to the Delta,” said the Bay Institute’s Rosenfield. “What has flowed out of the San Joaquin Valley is returned irrigation water which has high concentrations of agricultural chemicals and waste products and an unnaturally high level of the naturally occurring salts and toxic trace elements flushed by drain- age discharges from the soils of the San Joaquin Valley.”
Increasing the volume of fresh water from upstream in the San Joaquin Valley that makes it to the Delta “will improve water quality and enhance all the beneficial effects of freshwater flowing through the Delta,”
such as food web productivity, trans- port of fish and fish food and migration cues for fish, said Rosenfield. More water benefits the ecosystem by improving spawning and rear- ing habitat and by helping fish such as Chinook salmon, steelhead and sturgeon in their migration to and from the San Joaquin River and its tributar- ies, said Rosenfield.
“For any of these benefits to be fully realized, most of the restored San Joaquin River flow has to actu- ally make it from the river’s mouth through the Delta,” he said. “If all of the flow of the San Joaquin River is subsequently diverted at the south Delta export facilities, as has been the practice in the recent past, then many of the benefits of increasing flows will be neutralized.”
In 2000, the San Joaquin River Agreement sought to address San Joaquin River flow requirements through the Vernalis Adaptive Man- agement Plan, which examines the effects of flows and exports on mi- grating salmon. The Agreement was incorporated into the State Water Board’s Decision 1641, which allocated responsibility for the Vernalis flow and salinity requirements to the Bureau of Reclamation because of its large diver- sion of water from the San Joaquin River to eastside farmers and through its CVP deliveries to the west side of the San Joaquin Valley.
Kincaid said the State Water
Board’s approach to setting San Joaquin River flow objectives “is a bit different and, we think, unsupported.” “It appears that this time around,
the State Water Board will attempt to control flow at the reservoirs rather than measurement at a compliance point,” she said. “In so doing, the parties responsible for meeting the objectives appear to be limited to the parties who run water facilities such as the reservoirs. This is a problem because it violates the rules of water right priority and circumvents the secondary step of a water right hearing, by allocating responsibility for meet- ing the objectives in the first quasi- legislative step.”
The draft objectives for the San Joaquin River call for a percentage of unimpaired flow to be provided from the three principle tributaries to the San Joaquin, but also allow for adap- tive management of these flows to better protect fish and wildlife and reduce water supply impacts. Still to be determined is the flow contribu- tion from restoration efforts on the upstream San Joaquin River. Howard said it’s too soon to “jump in and fiddle with it right now,” and that it would be “premature” to call for water from a non-existent river channel. The issue will be revisited in a future State Water Board review of the Bay-Delta Plan, he said.
The Carquinez Strait, a narrow break in the Coast Range, connects Suisun Bay with San Pablo Bay.