Federal wildlife officials Friday ordered substantial cuts in water diversions from the Sacramento-San Joaquin Delta to protect a rare fish.

The order from the U.S. Fish and Wildlife Service came after dead Delta smelt have piled up at state and federal water diversion pumps since mid-December. The native species is protected by the Endangered Species Act and considered a bellwether for the health of the estuary.

The pumping systems near Tracy are operated by the U.S. Bureau of Reclamation and the California Department of Water Resources. Together, they deliver water to 25 million people and about 3 million acres of farmland from San Jose to San Diego.

Friday's order is not likely to result in immediate water shortages. But it does mean the agencies will have less water to put into storage for use in the summer.

More significantly, water diverters are inching dangerously close to an annual limit on the number of smelt that can be killed under Endangered Species Act rules. The rules allow 305 smelt to be killed at the pumps over the entire water year, which concludes Sept. 30. Already, the pumps have killed 232 smelt as of Wednesday.

This surpasses a 75 percent threshold that triggers talks between the agencies to find additional measures that may be necessary to protect fish.

"Those consultations are occurring," said Steve Martarano, spokesman for the Fish and Wildlife Service. He said it is the first time the threshold has been reached since new smelt rules were imposed in 2008.

If the limit of 305 is exceeded, the Fish and Wildlife Service would be compelled to impose new rules that could curtail water deliveries at critical times later in the year.

"We could see continued reductions and, yeah, that is a concern," said Roger Patterson, assistant general manager of the Metropolitan Water District of Southern California, the largest single consumer of Delta water for urban purposes. "These are not easy decisions, obviously."

The order does not specify pumping reductions. Rather, it requires DWR and Reclamation to minimize reverse flows in channels leading to the powerful diversion pumps. These reverse flows, which are contrary to natural flow dynamics, confuse fish and alter aquatic habitat.

The Fish and Wildlife Service first imposed modest pumping limits Dec. 17, after surveys showed smelt began dying at the pumps Dec. 12. The new limits ordered Friday will reduce pumping further.

The problem was apparently triggered, in part, by storms in December that caused the Sacramento River to swell, sending a pulse of muddy water downstream. Such "first flush" events do not occur every year, but are known to be a migratory trigger for smelt. The fish follow this turbid water upstream from Suisun Bay to begin their spawning season.

Because the pumps were diverting a lot of water then, the fish may have been lured into the south Delta by these flows, where they became isolated and vulnerable to the pumps.

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