Some very expensive salmon may be swimming in the San Joaquin River.

In the coming years, hundreds of millions of dollars will be spent on the river’s behalf.

Some predict restoration costs will surpass $1.2 billion. Others believe it will be half that much.

Whatever the final price, the money will come from farmers, Congress and ordinary Californians. It will pay for levees, fish screens, stream channels and more. And the benefits, proponents insist, will be enjoyed by humans and fish alike.

The work is the result of a settlement of a long-running federal court case — and a painstakingly negotiated agreement in Congress to carry out that settlement. Democratic Sen. Dianne Feinstein and Rep. Jim Costa, D-Fresno, were the lead authors of the final congressional bill.

Some projects, like building a salmon bypass channel around Mendota Pool in western Fresno and Madera counties, are to be done by 2013.

Many projects involve preparing the long-dry river channel so it can carry at least 4,500 cubic feet per second of water. By contrast, the flow immediately below Friant Dam currently bumps along at about 180 cubic feet per second.

Lower-priority projects are to be finished by 2016, including isolating or filling gravel pits north of Fresno.

Still other projects are up in the air. Most notably, there’s no agreement yet on what to do with a 22-mile stretch of the river near Los Banos called Reach 4B. The consulting firm CH2MHill estimated this stretch alone could require $375 million. Negotiators punted on fixing Reach 4B, calling for further study.

“Cost-benefit is one measure that will have to be considered when studying the feasibility of using this reach of the river,” Los Banos-area landowner Cannon Michael cautioned a House subcommittee in 2007. “It is important that you understand the challenge of moving fish through this reach.”

Some funds already being collected will be solely dedicated to the river restoration. Other funds still must be found.

East-side farmers now served by Friant Dam irrigation water currently pay about $8 million a year under a 1992 law. This “Friant surcharge” presently supports environmental improvements throughout the San Joaquin Valley. Under the settlement, the entire Friant surcharge will instead be focused specifically on San Joaquin River improvements.

Friant farmers, like other customers of the federal network of dams and canals known as the Central Valley Project, also pay an annual “CVP Restoration Fund” fee. This amounts to about $11 million annually from the farmers and finances environmental work throughout the Sacramento and San Joaquin valleys. The settlement will steer $2 million annually from Friant’s CVP Restoration Fund payments toward San Joaquin River restoration work.

Together, the Friant surcharge and restoration fund payments will provide $10 million a year for the San Joaquin River.

But that’s barely scratching the surface. Friant farmers also are repaying the federal government for construction of Friant Dam. These payments currently total between $10 million and $12 million a year, and go directly into the U.S. Treasury. Under the settlement, these Friant capital repayments will be dedicated solely to the river restoration until the dam is paid off, now scheduled for 2014.

Congress and California are pitching in, too.

In November 2006, California voters approved Proposition 84, the latest in a series of water bonds. The measure set aside $100 million to help implement the San Joaquin River settlement. In addition, state officials have indicated they can provide upwards of $100 million or so from another bond measure approved in 2006.

As part of the political deal-making to pass the river restoration bill, Feinstein included a provision requiring that state funds match federal spending. Which brings us to Congress.

The San Joaquin River restoration legislation authorizes — but does not provide — $250 million for the river work. Portions of this money will have to be sought each year through the appropriations process.

In essence, this could mean San Joaquin River funding requests will end up competing against other projects.

Should Congress fail to provide the expected funding, engineers would be forced to pick and choose which which parts of the project should be done. This would mean running the risk that the project could fail to meet its goals — and thereby reopen the dispute that led to the settlement.

Uncertainty about funding “is always a risk when you’re dependent on other entities to do their part,” said Alexandra Pitts, acting deputy regional director of the Fish and Wildlife Service. “But we would try to make do with what we had.”