The move is not expected to trigger immediate water shortages, but is likely to cause reservoirs such as Lake Del Valle near Livermore to be drawn down sharply this summer. That could affect boating and fishing at the popular lake.
State water officials say the shutdown is likely to be in place for seven to 10 days.
They could crank the pumps back on if water shortages develop or if Delta smelt, which have been killed at the pumps in increasing numbers since the weekend, move downstream and out of danger.
"People will have water. Nobody is going without water," DWR director Lester Snow said.
But Snow also emphasized that the Delta's ecology and its ability to meet state water demands are broken.
"If we don't fix the Delta, this is going to start happening every year," he said.
The decision to turn off the pumps comes as two court decisions -- one in April and one last week -- determined that the pumps are operating in violation of endangered species laws, and a week after new data showed that the population of Delta smelt, the most severely imperiled of a host of declining Delta fish species, plunged sharply downward.
That drop has led some biologists and environmentalists to caution that the fish could be approaching extinction. However, Department of Fish and Game Director Ryan Broddrick was not so pessimistic, saying, "I don't think they're at the edge of extinction. I would not ring the extinction bell."
State water officials say the last time the pumps were shut off was in 2004, when the Jones Tract levee broke and officials stopped pumping to reduce saltwater intrusion into the Delta. The time before that was in 1999, when the pumps were shut down because of high numbers of fish being killed.
The State Water Project operates the larger of two sets of pumps in the Delta near Tracy. It serves 25 million people, including residents of Southern California, Dublin, Pleasanton and Livermore, Santa Clara County, Fremont, Newark and Union City.
The smaller Central Valley Project serves millions of acres of farmland in the San Joaquin Valley. The federal government was expected to announce changes to its water deliveries later today.