Over the past five years, the delta smelt population has plummeted to the lowest levels ever recorded. In 2005, delta smelt abundance was the lowest ever measured, just 2.4% of the abundance measured when the species was listed under the state and federal ESAs in 1993. The 2006 and 2004 abundance levels were the second and third lowest, respectively. The species is now poised on the edge of extinction. Their numbers are so low that California Department of Fish and Game spring survey for larval fish is having difficulty even finding delta smelt this year.
The smelt are an indicator of the health of the Bay-Delta ecosystem, and are representative of a much larger decline in delta fisheries, including striped bass, longfin smelt, threadfin shad, and others. The delta functions as the hub of the state's water system, as a unique ecosystem, as a vital component in the state's fishing and agricultural economies, and as home, recreational mecca, and many other things, for millions more Californians. As stated in the recent PPIC report on the delta: "Most Californians rely on the Delta for something, whether they know it or not." 
The recent decline of the species coincides with significant increases in freshwater exports out of the delta by the state and federally operated water projects. Annual exports have increased 25% from 1994-1998 and 2001-2006, draining the delta of more than 1.2 million acre-feet of additional water. Annual exports in 2005 and 2006 were the first and third highest exports levels on record. Wintertime exports have increased by 49% from 1994-1998 and 2001-2006, and springtime exports have increased by 30%. Delta smelt are particularly vulnerable during winter and spring, when pre-spawning and spawning adults move into the delta for reproduction, and larvae and juveniles move downstream to rearing habitat.
Freshwater exports were identified as a significant threat to the species when it was listed in 1993. Recent research by a team of interagency scientists confirms that freshwater exports remains one of the primary causes of population decline of delta smelt and three other delta fish species. Despite this, the 2004 plan by state and federal water project agencies to increase exports even more was approved by US Fish and Wildlife Service in their biological opinion. This "no jeopardy" conclusion has been challenged in court by several environmental and fishing organization.
Take reported for delta smelt at the state and federal pumps is known to grossly underestimate the number of fish killed at the pumps. First, fish smaller than 20 mm in length, which includes most smelt larvae and juveniles, are not counted. The USFWS estimates the loss of larval and juvenile delta smelt to entrainment as several million each year. Second, many more fish are lost to predation or pass through the fish salvage facilities to the pumps uncounted.
More than 80% of California's surface water withdrawals are used for irrigation. About 15% is used for public, municipal supply.
Pumping needs to be reduced. The agencies involved in operating the pumps and the agencies charged with protecting the fish all recognize that certain steps must be taken, that aren't being taken. The March 2007 Pelagic Fish Action Plan prepared by DWR and DFG identifies a number of minimum steps that should be implemented to protect the smelt, but aren't. The Delta Smelt Working Group has identified a number of measures that would be helpful to smelt, but the WOMT (the project operators) have either refused to implement them, or the working group has declined to require them for fear that they would run out of "environmental water" to use later in the year, when the need might be greater. This is an unlawful approach. The ESA requires the agencies to make sufficient water available to protect and restore the smelt, whether it's set-aside as "environmental water" or not, and whether it would have an adverse impact on project operations or not.
 Public Policy Institute of California, Envisioning Futures for the Sacramento-San Joaquin Delta, at 4 (2007).