DELTA SMELT (Hypomesus transpacificus)


The small, nearly translucent delta smelt is endemic to the west coast’s largest estuary, the San Francisco Bay and Sacramento-San Joaquin Delta. The Delta drains California’s Central Valley and is formed by the confluence of the south-flowing Sacramento River and the north-flowing San Joaquin River, just east of where they enter Suisun Bay, an upper arm of San Francisco Bay. The Delta encompasses 1,600 square miles and drains over 40 percent of the state. The Delta provides habitat for numerous species of fish and wildlife. Nearly half of the state’s migrating waterfowl and shorebirds and two-thirds of the state’s spawning salmon pass through the Delta.

US Fish and Wildlife Service photo

Delta smelt are found only in shallow open waters of the upper reaches of the Delta. Delta smelt require specific freshwater flow, water temperature and salinity, and habitat types to complete their migration, spawning, egg incubation, rearing, and larval and juvenile transport from spawning to rearing habitats. Throughout most of their lifespan, delta smelt inhabit low salinity habitat at the interface of inflowing fresh water from the Sacramento and San Joaquin Rivers and salt water from the Pacific Ocean. Spawning adults, larvae and young juveniles are found farther upstream in the Delta. Delta smelt are a potent indicator species for gauging the health of the Delta ecosystem.


Of the original 29 indigenous fish species in the Delta, 12 have either been eliminated entirely, or are currently threatened with extinction. Many of the fish species in the Delta are in rapid decline and scientists are now warning of an ecological crash of fish populations and the Delta food web. These population declines are attributed to a combination of factors including increasing water diversions for export, loss of habitat, increased competition and predation from introduced species, and impaired water quality due to pesticides and other pollutants.

Once one of the most common and abundant of the pelagic fishes in the Delta, the delta smelt population is estimated to have declined approximately 90 percent in the last 20 years. As a result of a severe population decline in the 1980s, the delta smelt was listed as a threatened species under the Endangered Species Act in 1993. The recent trend from continual decline to catastrophic collapse of the Delta’s pelagic fishes, including delta smelt, longfin smelt, threadfin shad and striped bass, began around 2002. Numbers of white sturgeon and green sturgeon in the Bay and Sacramento River have also fallen to alarmingly low levels since 2002. The Center petitioned for Endangered Species Act listing of the green sturgeon population in 2000, and the National Marine Fisheries Service proposed listing the San Francisco Bay population as threatened in April 2005.

US Geological Survey Photo

By 2002 the delta smelt population had dropped drastically: more than 80 percent in just three years. In 2005, abundance of delta smelt plummeted to the lowest levels ever recorded, just 2.4 percent of the abundance measured when the species was listed in 1993. Recent surveys indicate that the ecological conditions in the delta smelt’s critical habitat, the upper Sacramento-San Joaquin Estuary, have also declined, threatening the planktonic food web upon which the species depends. Based on recent population viability and extinction risk analyses, the delta smelt has fallen below its “effective population size” and is in imminent danger of extinction. In March 2006 the Center, The Bay Institute and Natural Resources Defense Council petitioned the U.S. Fish and Wildlife Service to change the federal listing status of the delta smelt from threatened to endangered, on an emergency basis. In May 2007 the Center filed a notice of intent to sue the Service for failing to respond to the petition. In February 2007 these groups also petitioned the California Fish and Game Commission to change the state listing status from threatened to endangered. Fish and Game recommended that the Commission not take emergency action but rather proceed with a standard rulemaking for the delta smelt. In April 2007 the Commission denied the request for emergency action and Fish and Game recommended a positive 90-day finding on the state petition. In May 2007, after surveys revealed a juvenile smelt population crash of 92% from the previous low of 2006, the Center sent a request letter to the Commission to reconsider emergency endangered status.


Massive diversions of freshwater from the Delta, toxic pulses of pesticides and other pollutants from Central Valley agriculture, and predation and competition for food resources from introduced species are thought to be the causes behind the declines of delta smelt and other Delta fish species.

The Delta is a major hub for California’s water management system and supplies water to a region of intensive irrigated agriculture. The estuary has been plumbed to provide millions of acre-feet of water for export each year. Water diversions by the State Water Project, the federal Central Valley Project and private diversions in the Delta and its Sacramento and San Joaquin River watersheds take as much as 65 percent of the Delta’s total freshwater inflow during periods when the delta smelt population is distributed in the Delta. At times, pumping levels are so high they reverse the flow of the San Joaquin River, confusing and delaying up-migrating adult fish and impairing downstream transport of larval and juvenile delta smelt from the upper estuary where they were spawned to their brackish water rearing habitat.

High levels of water exports have consistently corresponded to low delta smelt abundance. Water pumping not only alters smelt habitat by reducing freshwater inflow, but the pumps and diversion facilities kill millions of fish each year, including a large percentage of larval and juvenile delta smelt. The recent decline of delta smelt and other Delta fisheries coincides with significant increases in Delta water exports by the state and federal water projects (seasonal water exports in the 2000s are as much as 48 percent higher than in the early 1990s) and higher mortality of delta smelt by the pumps. The four highest years of water exports from the Delta have occurred since 2000.

All life stages of delta smelt are at least periodically exposed to lethal or sub-lethal concentrations of herbicides and pesticides discharged and transported from upstream into their habitat, and chemicals may also have indirect effects on their Delta ecosystem. There is growing evidence that fish species in the Delta are suffering direct mortality and physiological and/or developmental impairment from the presence of toxic substances in the water. The plankton upon which the smelt feed may also be declining due to periodic, highly concentrated pulses of pesticides through the Delta. Read a Center report on pesticide impacts to Bay Area endangered species, Poisoning Our Imperiled Wildlife: San Francisco Bay Area Endangered Species at Risk from Pesticides.

Invasive species may also play a role in the fish declines. Introduced fish such as bass and threadfin shad may have increased predation on delta smelt and compete for their plankton food. An invasive clam, Corbula amurensis, has reduced the abundance of the delta smelt’s plankton food supply and may affect the feeding efficiency and growth of delta smelt larvae.


Incredibly, in the face of crashing fish populations, the state and federal agencies charged with protecting the fisheries under the state and federal Endangered Species Acts have failed to protect the Delta’s fish populations and have given approval for increased water diversions and water storage projects. For example, the proposed “South Delta Improvement Program” will increase Delta water exports and install permanent tidal barriers that would further modify Delta flow patterns and alter smelt habitat. The CALFED Bay-Delta Program, promoted as a solution to reducing the negative impacts of the federal and state water projects on fish and wildlife, has proven ineffective and now has largely collapsed. The Fish and Wildlife Service’s most recent Biological Opinion for protection of the species relies nearly exclusively on the CALFED Environmental Water Account, an experimental fish protection tool that, after five years of implementation, has failed to provide detectable benefits for delta smelt or any other fish species.

The Center and other conservation and fishing groups have a different vision of a restored Delta ecosystem and are fighting to reduce water exports, reverse the declines of fish populations and protect the ecology of one of the world’s greatest estuaries.



May 24, 2007
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