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June 1999
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Sewer of Dreams

In the wake of a mid-May U.S. Supreme Court announcement, some environmentalists and fish biologists are allowing themselves to imagine a scenario that for half a century has been virtually unimaginable: native salmon returning to the upper reaches of the San Joaquin river. The rulingis just one of a string of current developments and initiatives that could help improve flows, habitat and water quality in the much-abused San Joaquin.

The high court let stand a 1998 appeals court decision requiring the Bureau of Reclamation to operate Friant Dam in compliance with California environmental protection laws, and invalidating 14 long-term federal contracts for water diverted to irrigators through the Friant-Kern and Madera canals. The contracts must now be renegotiated subject to a full review under state and federal environmental protection laws, says Hal Candee of the Natural Resources Defense Council (NRDC), which first sued BurRec in 1988.

If water is eventually released from Friant Dam it could mean a virtual rebirth for a river that is often described as little better than an open sewer. The San Joaquin was identified in 1997 as one of the most threatened rivers in the nation by the organization

American Rivers due to low flows, pollution and encroaching urbanization. Farmers who rely on the San Joaquin's water feel equally threatened, however, fearing that they may be forced to retire thousands of acres of productive farmland for lack of irrigation.

One of California's two main riparian arteries, the San Joaquin runs nearly 200 miles from its headwaters east of Fresno to the Delta. When the BurRec built Friant Dam - part of the federal Central Valley Project - in 1941, the intention was to divert virtually the entire flow of the river into canals to irrigate southern farmland. Some water was left in the river for the 35 miles between Friant Dam and Gravelly Ford to appease existing riparian water rights holders. However, water project managers opted not to continue allowing river water to flow over the porous riverbed at Gravelly Ford, where much of it would percolate into the groundwater and be "lost." As a result, for a 20-mile stretch from Gravelly Ford to Mendota Pool the river is bone dry, except in flood years. And that, says John Cain of the Natural Heritage Institute, is the primary reason why salmon cannot get to their spawning grounds in the upper San Joaquin. There is still water in the river for the 35 miles above Gravelly Ford that could provide spawning habitat, he adds.

Conditions aren't great below Mendota Pool, either. In 1951, water engineers built the Delta Mendota Canal to bring water from the Delta to Mendota Pool. From there, the water flows into irrigation canals and the river itself. Rights holders below Mendota Pool, the San Joaquin Exchange Contractors, essentially traded river water for Delta water. Downstream from Mendota Pool, the river consists primarily of irrigation return flows. Because of the poor conditions, a fish barrier at the San Joaquin's confluence with the Merced River diverts salmon up that tributary to protect them.

NRDC's case now goes back to the district court in Sacramento, where a judge will decide how much, if any, water must be released from Friant Dam to protect salmon. Behind the scenes, however, NRDC and the Friant Water Users Authority are continuing confidential settlement negotiations begun last fall. "We have explained to the court that we are exploring ways to restore flows below Friant Dam and associated public trust values on a mutually acceptable basis," says Candee.

In the meantime, the Natural Heritage Institute has put forward a proposal for rewatering the San Joaquin that combines a water-swap scheme that has been around for decades with a groundwater banking plan. The proposal involves sending some of the Delta water now used by the Exchange Contractors to Friant water users through the California Aqueduct. In exchange, water would be released from Friant Dam into the San Joaquin. "As the river flows its natural course, it would recharge the aquifer, which could be tapped in dry years to meet the Exchange Contractors needs," explains Cain. The idea is getting an enthusiastic response from some stakeholders. "We have been proposing large scale recharge using wet year water for years," says Ed Steffani of Stockton East Water District. "We have a huge underground reservoir here - more than 3 million acre-feet-just waiting for water."

Back to the NRDC's case, it's unclear what effect, if any, the outcome might have on CALFED and other ongoing negotiations. "We would be happy to amend the Ecosystem Restoration Program Plan if the courts restore flows to the San Joaquin," says CALFED's Dick Daniel. "But to start making those plans now would be premature."

The legal drama is playing out against the backdrop of ongoing State Board hearings to determine which Valley water rights holders will be required to give up how much water to provide flows through the Delta in compliance with the Bay-Delta Accord. Those hearings are expected to last for at least another year. In the meantime, some of the major players have been negotiating among themselves and have devised a couple of plans that could improve conditions for salmon and other San Joaquin species.

Under the Vernalis Adaptive Management Program (VAMP), a 12-year experiment designed to determine whether low flows in the river or high exports from the Delta have a greater impact on fish mortality, flows at Vernalis (downstream of the confluence with the Stanislaus River) would be set at specific levels during the spring fish migration period, depending on the type of water year. The experiment is predicated on obtaining the necessary flows through the San Joaquin River Agreement, under which the biggest water rights holders on the river and its tributaries would provide up to 110,000 acre-feet of water a year for the VAMP experiment. The agreement is to be financed through a combination of state and federal funds, including if necessary the Central Valley Project Improvement Act Restoration Fund.

The latter provision irks some environmentalists, who don't like the idea of restoration funds being used to pay for water that they say the districts are legally required to release anyway under the Clean Water Act. However, since resolving this question would almost certainly entail years of legal wrangling, others feel it's a compromise worth making. Besides, as Natural Heritage's David Fullerton notes, "part of the agreement is that all parties will make a good faith effort to find alternative funding sources so that we don't have to dip into restoration money."

Others have different doubts about the plan. "While we support the intent of the VAMP studies, we're not convinced that any new or useful information will be generated," says Tim Ramirez of the Tuolumne River Preservation Trust, which is involved in a major restoration effort on the San Joaquin's largest tributary. "In addition, the way the VAMP flow requirements are met is to manipulate flows on the tributaries, which potentially compromises similar studies evaluating smolt survival on the Tuolumne." Ramirez adds that because the VAMP experiment requires large numbers of hatchery fish, he believes it increases pressure to establish a hatchery on the Tuolumne, a project he and others oppose. "We are trying to restore a river and a wild salmon population, not manage an aquarium."

The agreement has also encountered opposition from some Delta interests, who fear that the vamp's spring pulse flows may reduce the amount of fresh water released into the river in late summer, when low flows, discharges and contaminated agricultural drainage already create severe water quality problems in the lower part of the river. Nevertheless, VAMP has the support of both the City of Stockton and the Stockton East Water District, according to the District's Ed Steffani, who says studies to determine the agreement's effect on water quality are being conducted. "There has been a very good cooperative effort to make this thing work so that no one gets hurt," he says. Natural Heritage's Fullerton adds that in the continuing negotiations over the final form of the agreement, "efforts are being made to give assurances that flows won't be reduced in the summer."

The poor quality of San Joaquin water is almost legendary, and is the focus of two new Central Valley Regional Water Quality Control Board initiatives. In January the Board launched a steering committee to guide the development of total maximum daily loads allowable for the river (TMDLs) of the constituents that contribute to low dissolved oxygen in the water column. These biochemical oxygen demanding substances (BODs) are organic substances found in both municipal waste water and agricultural runoff, according to the Board's Tom King. The Board is currently seeking funding for the necessary studies, which it hopes to begin in December.

Perhaps none of the San Joaquin's water quality problems has been as confounding as the poor drainage and mineral laden soils that leach salt, selenium, boron and other contaminants into the river with agricultural runoff. Salt concentrations in the lower part of the river exceed water quality objectives approximately 50% of the time during the spring and summer, according to the Regional Board's Rudy Schnagl. As Stockton East's Steffani explains it, "We pump salty water from the Delta to the westside, where they irrigate salty land with it. The runoff goes to the river and then into the Delta and we turn around and pump it back again. The salt problem gets worse almost exponentially."

This spring, the Board held a series of public workshops on a proposed Basin Plan Amendment for salt and boron in the stretch of the river from Vernalis to Mendota Pool, a move that has been greeted with enthusiasm by water users in the lower part of the river. "The Board's stated objectives to set water quality objectives above Vernalis by the end of the year is a giant first step," says Steffani. "We've been trying to get them to do that for literally 30 years."

According to Schnagl, the Board is focusing on the types of in-Valley solutions identified by the San Joaquin Valley Drainage Program in a 1990 management plan, such as irrigation improvements and drainage reuse. However, some observers believe that these measures will ultimately be fruitless.

"The only way we are going to solve the San Joaquin and Delta water quality problem and still farm as many acres as we do is with an ag drain" to carry contaminated water out of the valley altogether, says Steffani. "The farmers can't really solve the problem themselves because we're supplying them with salty water." The mere mention of a drain has caused political fireworks for decades, as it harkens back to the San Luis Drain closed by the Kesterson wildlife refuge environmental disaster years ago. Steffani acknowledges that draining to the Delta, the Sacramento River or Monterey Bay would be politically and environmentally unfeasible. Instead he advocates biting the financial bullet and constructing a drain that would carry waste water far out into the deep ocean.

Although recent developments seem to offer glimmers of hope for the San Joaquin, some fear that urbanization along the river's banks may erase any gains. "If we can't preserve a river corridor, hopes for restoration will be lost," says Natural Heritage's John Cain, pointing to new developments such as Gold Rush City as an example of the creeping threat. Indeed, the idea of restrictions on land use is so politically sensitive that until recently, few dared even whisper the thought. But that may be changing, thanks to the floods of 1997. The Army Corps of Engineers is conducting a comprehensive study of the San Joaquin and Sacramento Basins and developing a plan to improve both flood management and ecosystem restoration. The plan is likely to include measures such as dam reoperation and flood plain restoration, as well as possible restrictions - or at least disincentives - on development in the flood plain, according to the Corps' Steve Yaeger. Any such restrictions would have to be approved by both the state and federal governments. Nevertheless, says Yaeger, "we think we can put together a pretty compelling package that combines flood plain management, flood damage reduction and ecosystem restoration."

Other improvements to the river's habitat for fish and wildlife may be accomplished by the San Joaquin River Riparian Habitat Restoration Program, a program launched by those already negotiating on the flows issues. Joining forces in the program are NRDC, the Water Users Authority and the Pacific Coast Federation of Fishermen's Associations. "We decided that we should see if we could find opportunities to work together to help the river," says the Authority's Dan Fults.

The program's objective is to develop a restoration plan for a continuous riparian corridor in the reach of the river between Friant Dam and the Merced. "If fish ever get up there they will need riparian habitat to supply food and shading," says the program's Paula Landis. "But right now we're not talking about fish. We're just talking about habitat that can provide important benefits to all kinds of species, including endangered species like the yellow-billed cuckoo and the riparian brush rabbit," of which fewer than a hundred remain in the state.

The program launched in 1997, has identified 15-20 specific projects and begun implementing several of them. But participants say it has also had a less tangible benefit. "Working together on this has helped to build trust among the parties," says Fults.

If flows are regained, habitat restored and water quality improved, would salmon return to the San Joaquin? You bet, says U.C. Davis biologist Peter Moyle, who says a certain number of migrating salmon naturally stray into new habitat every year. "If you give them the water, they'll come," he says, adding "five years ago this conversation would have been a pipe dream. It's amazing that we are even able to talk about it."

Contact: John Cain (415)788-0550, Paula Landis (559)487-5103 or Ed Steffani (209)948-0333

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