The water system through the Sacramento-San Joaquin Bay-Delta region has large metal screens in place at the Skinner facility to protect fish from being sucked through large pumps. California state officials said six indicator Delta fish species are in decline.
The latest trawl-net fish count shows the population of California's six species of Sacramento-San Joaquin Delta fish are dwindling.
A population crash started in 2002 for the six species, including the protected Delta smelt. A wet winter in 2011 halted the decline.
But the Sacramento Bee reports the California Department of Fish and Wildlife count in fall 2012 shows those gains have been erased.
All six species returned to their prior low numbers. One species, threadfin shad, set a record low population in the latest survey.
"In a nutshell, we just went back to the baseline and it's not particularly good," said Randy Baxter, a supervising environmental scientist at the Dept. of Fish and Wildlife.
Baxter told the Bee that 2012 was a relatively dry year, which may have contributed to the latest decline. Less rain and snowmelt runoff mean less aquatic habitat, less water to dilute pollutants, and changes in the way food is produced and available to fish.
The big controversy still clusters around freshwater flows into, and out of, the estuary. These flows are tightly controlled by California's vast network of dams, canals and pumps and the demands of the people and crops that depend on that infrastructure.
The Delta fish population is considered an important barometer of estuary health.
The Delta river water is a main source of California's supply and the water is shared by urban dwellers and the agriculture industry.