But last month, scientists unveiled a pair of theories that might help explain the crisis, or at least guide investigations next year. Neither theory fully explains the crisis. Together they might.
Theory No. 1 supposes conditions in Suisun Bay and Suisun Marsh, which are important development areas for young fish, have deteriorated because of the invasion of the "overbite clam."
The clam, which is native to Asia and arrived in the San Francisco Bay in ship ballast water around 1986, is a prodigious filter-feeder that consumes the zooplankton that young fish need. The clam grows in extremely dense colonies and thrives in brackish water that is saltier than is common in the Delta.
But the Contra Costa Water District, along with scientists from other agencies, has found that salinity in the Delta has increased during the fall during the past 10 years.
That might be contributing to the spread of clams, which in turn could be wiping out the food supply for young fish.
Theory No. 2 says that a move about 10 years ago to protect Delta fish by shifting the timing of water pumping from spring to fall and winter might have had the unintended effect of killing large numbers of fish.
The number of fish turning up at the pumps has skyrocketed during winter in recent years, and so has the density.
Scientists only recently discovered the higher fish salvage rates in the winter, but they say the numbers are striking.
So far, they do not have an explanation for the change. But among the possible explanations is that the fish are moving upstream in the Delta and closer to the pumps in search of food.
Still, scientists have not discounted any of the possibilities they began exploring earlier this year, including:
Pesticides from the Central Valley and particularly a new class called pyrethroids that are becoming more common because they are safer for mammals. Pyrethroids are also more toxic to fish, although they tend to not remain in water for long periods of time. Also, a toxic algae called Microcystis is appearing more in the Delta and is attracting scientific attention.
Invasive species, including zooplankton and weeds that are slowing down water and changing habitat for Delta fish.
Scientists expect to spend about $3 million next year on further investigation, but it remains unclear when they will have any definitive answer.