Poor oceanic feeding conditions and commercial fishing have been identified as key causes of the collapse of Sacramento River fall run Chinook salmon.

According to the National Marine Fisheries Service, immediately prior to the sharp salmon decline in 2007, rising temperatures in the Pacific Ocean depleted much needed nutrients. Salmon that spend most of their life in ocean waters can be decimated by the lack of food available as a result of changing ocean conditions. As a result, oceanic conditions can have dramatic impacts on the salmon runs in the Delta from year to year.

Sacramento River fall Chinook (not listed per the Endangered Species Act) has traditionally been considered the primary salmon stock supporting California ocean fisheries, historically comprising 80-95 percent of the salmon catch. In 2003 at the height of commercial salmon fishing in California, Chinook Salmon ocean harvest totaled 6,391,621 pounds. (In 2011, only 990,977 Chinook Salmon were harvested.)  This dramatically reduces the number of salmon returning upriver to spawn and increased the prevalence of hatchery born salmon released to the wild.

In comparison, a study by the Department of Water Resources found that only 0.4 percent of Delta salmon are lost directly at the Delta pumps.

The winter-run Chinook has particularly struggled.  Unlike the popularly fished fall-run and spring-run, the winter-run is endangered.  While there are restrictions on the taking of the endangered winter-run, it can be nearly impossible for fishermen to distinguish between winter-run and fall-run at the time of harvest.  This leads to the inevitability that as more fall-run are harvested, increasing numbers of already scarce winter-run will be lost as well.

Fishbio reported that the Pacific Fisheries Management Council (PFMC) uses an outdated and highly inaccurate model to predict salmon abundance on the West Coast.  The Salmon Technical Team uses data on the number of fall-run Chinook jacks (two-year old fish) that returned to the Sacramento River the previous fall to calculate a forecasted index of abundance, called the Sacramento Index (SI).  The SI is the number of adult fish projected to be available for ocean harvest or that will escape to the Central Valley. PFMC uses the SI to set annual fishing regulations.

Since 2005, PFMC has overestimated the SI nine times.  In 2012 and 2014, the Salmon Technical Team attempted to develop more accurate forecasting methods. Each new forecast was closer to actual numbers, but still inaccurate.

The Salmon Technical Team expressed concern that setting high harvest limits for fall-run Chinook based on overly optimistic estimates may increase the bycatch of endangered Sacramento River Winter-run Chinook salmon in the fishery.