California Sea Lions are abundant, widely distributed and experiencing population increase through most of their range. They were historically important to native people living in coastal areas and on islands used by sea lions for rookeries. Huge middens in southern California and on the Channel Islands, with large numbers of California Sea Lion and other pinniped bones, attest to the past importance of marine mammals in subsistence cultures prior to the changes that followed the arrival of Europeans on the west coast of North America (Porcasi and Fujita 2000). In the 19th and early 20th centuries, California Sea Lions were harvested intensively for a variety of products, and hunted for bounties to reduce their impact on fisheries (Cass 1985).

California Sea Lion mortality occurs in conflicts with fisheries, by poaching, and through entanglement in marine debris (Stewart and Yochem 1987; Aurioles-Gamboa et al. 2003). Prey availability is greatly reduced during El Niño events and large numbers of pups born during these periods die of starvation, as do weaker animals from all age classes (Francis and Heath 1991). The sea lion rookeries inside the Gulf of California do not appear to be greatly effected by El Niño events (Aurioles and Le Boeuf 1991; Wielgus et al. in press).

California Sea Lions accumulate pollutants through the food chain, and large amounts of DDT, and PCBs discharged in the past, continue to accumulate in coastal marine food chains that include this species. Additionally, large amounts of agricultural and urban runoff and waste continue to be discharged into coastal marine habitats annually from numerous sources; this may have effects on sea lion immune systems and overall health. California Sea Lions do sometimes die of paralytic shellfish poisoning caused by domoic acid, a biotoxin produced by diatom blooms that enter the food web through planktivorous fish such as herring and sardine (Silvagni et al. 2005). California Sea Lions experience mortality from a number of diseases, including some such as leptospirosis contracted from terrestrial animals. They are at risk of exposure to additional diseases from contact with feral and domestic dogs and other terrestrial animals.