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The San Joaquin River was nearly as grand. High up in the Sierra Nevada, it began as a trickle, and rapidly gained volume as it flowed into the Central Valley. There, it merged with the Merced, Tuolumne, Mokelumne, and Stanislaus rivers. This confluence of water once created giant marshes that attracted untold numbers of fish that would swim upstream into the mountains and back out to sea.
These powerful rivers once made the Delta a predominantly fresh body of water: Records from the early 1900s kept by the C&H sugar factory show that freshwater could often be drawn from as far west as the Suisun Bay, near the Carquinez Strait, which separates the East Bay from the North Bay.
However, during the past century, the state erected numerous dams on the rivers and their tributaries, so as to divert freshwater to farms and cities. In turn, water diversions have continuously increased since the 1950s. In 2011 alone, the state removed more than 6.3 million acre-feet of freshwater from the Delta and sent it south — the equivalent of about 2 trillion gallons. Between January 2012 and May of this year, the Tracy pumps sucked 5.3 million acre-feet of freshwater out of the Delta.
The San Joaquin River currently carries just a little more than 30 percent of its natural flow of water. In some years, the state diverts 90 percent of its water (sixty-mile stretches of the river have run dry at times). As for the Sacramento River, it carries about 70 percent of its natural flow of water to the Delta on average.
The removal of all that freshwater — both from rivers before they reach the Delta and from the Delta itself — has allowed saltwater from San Francisco Bay to dominate parts of the region. Large volumes of saltwater now often extend as far inland as Antioch, some twenty miles east of the old salt line near the Carquinez Strait.
The saltwater intrusion has been especially bad for fish: It has reduced the freshwater habitats in the Delta, which many fish need to reproduce; it has decreased the amount of dissolved oxygen in the water, which fish need for survival; and it has made the Delta's water less cloudy with sediment, which has exposed smelt and other threatened fish to predators. All of these factors have led to sharp declines in fish populations and a multitude of environmental problems.
The ecological damage caused by large water exports is most evident on the San Joaquin River. In 2010, the state water board commissioned a wide-ranging study and found that, in order to protect fisheries and southern Delta farmers, 60 percent of the San Joaquin River would need to flow into the estuary. However, after factoring in the needs of San Joaquin Valley agriculture and Southern California water users, the water board dropped that number to 35 percent. The San Joaquin River, in other words, is one of the most endangered rivers in the nation. "It is just a cesspool, it's horribly overdeveloped," said Rosenfeld of the Bay Institute, referring to the San Joaquin and the huge amounts of water the state takes out of it. "And, as a result, the southern Delta is also a cesspool."
The Sacramento River still has pretty powerful flows, though, making water quality not as big of an issue in the North Delta. But BDCP may change that. The two giant water tunnels are designed to divert up to 6.5 million acre-feet of water a year from the Sacramento River, and would have the capacity to eventually carry up to 11 million acre-feet annually. In addition, the state would continue to operate the Delta pumps in Tracy at about 50 percent of their capacity on average, and at 75 percent of capacity during dry years.
By removing so much freshwater from the Sacramento before it reaches the Delta, water quality could dramatically deteriorate in some parts of the estuary. "If we do the same thing to the Sacramento River that we've done to the San Joaquin, the balance in the Delta will start to salt up," said Loben-Sels. "The Sacramento River is what keeps us fresh."
In an April report, officials from the US Fish and Wildlife Service accused the state of not only skewing data to artificially boost the benefits of the 120,000-acre habitat restoration project, but also of glossing over the negative impacts of removing all that freshwater from the Sacramento River before it reaches the Delta. The basic takeaway from the report was that, while the most recent BDCP proposal is an improvement over past plans, weakened flows in the Sacramento River would likely result in "increased agricultural runoff, invasive aquatic vegetation, warmer temperatures, and increased algal productivity" — all of which would benefit invasive species over native ones.
The Sacramento River also is the most important contributor of sediment to the Bay-Delta region, especially during heavy rains and spring snowmelts when the river is carrying lots of freshwater. The twin tunnels, however, would divert this sediment-rich water during high flows. "Besides potentially negative effects on Delta smelt and Longfin smelt and their habitat ... clearer water would encourage growth of exotic aquatic plants ... in many areas of the North and West Delta," Fish and Wildlife wrote in its April report.