René Reyes, U.S. Bureau of Reclamation

Longfin smelt, ventral view

Water restrictions that have parched farms, lawns and pools in recent years to help save delta smelt from extinction could be expanded to provide similar protections to a larger species of smelt that has different habitat needs.

The U.S. Fish and Wildlife Service (FWS) agreed in court this week to reconsider a proposal to provide stringent Endangered Species Act protections to the San Francisco Bay and upstream population of longfin smelt.

Smelt were once abundant in the San Francisco-San Joaquin Delta, where they ate tiny plankton and grew into food for larger fish and other wildlife, but numbers of the small silver fish have crashed to precariously low levels.

The delta smelt is listed federally as a threatened species, forcing state and U.S. agencies to curtail the amount of water they pump to their customers out of rivers that carry rain and melted snow from the Sierra Mountains to San Francisco Bay. Smelt are killed by the pumps, and their breeding is disrupted by freshwater exports, which dry out the river system and cause its water to grow more salty.

In 2009, about 500,000-acre-feet of water originally destined for farms, businesses and homes was left in the delta in order to protect the threatened delta smelt, FWS figures show. That's enough water to quench nearly 1 million Californian households for a year, although much of the water exported from the delta is used on farms and in factories.

Water customers were forced to curb their use of delta water by an additional 1.6 million acre feet in 2009 because of drought conditions that were unrelated to delta smelt protections.

A previous study by the service found in 2009 that the delta’s population of longfin smelt, which are slightly larger and swim further up- and down-stream than delta smelt, did not warrant protection under the U.S. Endangered Species Act because it’s part of a larger population that inhabits West Coast streams as far north as Alaska.

Californian environmental nonprofits The Bay Institute and the Center for Biological Diversity challenged that finding in court, however, arguing that the delta population is so distinct from smaller populations found further north that it qualifies for endangered species protection as a distinct population segment.

The Endangered Species Act calls for endangered populations of wildlife to be protected if they are separated from other populations.

A judge on Tuesday approved a settlement agreement in the case that will see FWS again study whether the delta’s population of longfin smelt should be listed as a federally endangered species by studying the entire West coast population and considering whether the local population meets the legal definition of a distinct population segment. The previous study primarily considered whether the local population is a distinct subspecies. The FWS agreed to complete its study by the end of September 2011.

Providing Endangered Species Act protections to the delta’s population of longfin smelt could exacerbate cuts to the amount of water that can be pumped to customers out of the delta near Tracy because the species occupies different parts of the waterway and has a different lifecycle than delta smelt.

“They have slightly different locations in the delta, so depending on where they are and what kind of [rain and snow] you’re having, it could result in additional water supply restrictions,” said Laura King Moon, assistant general manager of the State Water Contactors, which represents 27 public agencies that use water drawn from the Delta.

“You might have to cut back pumping once for the delta smelt and then you might have to stop pumping for another month because you’ve got the longfin,” King Moon said.

While delta smelt occupy a small geographic range upstream from San Suisun Bay, longfin smelt can tolerate a wide range of salt levels and swim from freshwater at Rio Vista and Medford Island near Stockton all the way west to the Golden Gate and out into the marine Gulf of the Farallones.

Despite the populations’ vast population range, attorneys for the nonprofits argued that they are not known to significantly mingle or interbreed with the nation’s other longfin smelt populations.

“There has been little genetic study of the fish, and that’s mostly because they’re hard to find,” said Bay Institute scientist Jon Rosenfield, who argued that the fish are too small and weak to travel great distances through the ocean.

“In the absence of genetic evidence, which would be ironclad, we have to rely on the best professional judgment of biologists. To a fish biologist, you look at the San Francisco estuary and see that it’s relatively isolated from similar habitats further to the north. The prevailing current would be expected to carry fish from here to the north, but there isn’t a similar function of fish coming from other populations down to here,” he said

Protecting the longfin smelt, which was once one of the most abundant fish in the delta, from extinction by reducing water exports would help provide food for other wildlife. It would also increase freshwater flows to more natural levels through the delta and into the bay, which would benefit a wide range of native wildlife species.