San Diego fishermen fish sustainably. This means they leave enough fish in the ocean without affecting the future health of the stock while minimizing impacts on habitats and non-targeted organisms (i.e., bycatch). This sustains healthy marine ecosystems. To ensure fish and shellfish stocks remain healthy and vibrant, two approaches to regulate fishing effort are used: input and output controls.

Input controls limit the amount of fishing pressure going into the fishery, such as capacity, areas fished, and seasons. Two examples of input controls are limiting the number of lobster traps and setting the lobster fishing season. Output controls directly limit the quantity of fish or shellfish removed. These can be in the form of quotas such as the number of fish taken on an annual basis (e.g., annual catch limits) or the number of trips taken, and size limits. Output controls can also be seen as a way to limit by catch. These harvesting conditions ensure that San Diego fishermen provide consumers with responsibly harvested seafood.

San Diego fishermen bring 120 species of finfish and shellfish to port annually. For finfish, these landings include highly migratory species such as yellowfin tuna, bigeye tuna and swordfish; coastal pelagic species include sardine, Pacific mackerel and market squid, to more bottom dwelling and mid-water column groundfish species such as California halibut and around eight varieties of flatfish, and over 35 species of rockfish. Shellfish species landed include seven crab species, two types of sea urchins, market squid, and the most valuable, California spiny lobster.

Fishermen catch rock crabs, California halibut, rockfish, Pacific mackerel, sharks, opah, and tuna species such as yellowfin and bigeye year-round. Some species also have peak seasons like bluefin tuna, which can occur year-round but most prominently in coastal waters from June through September. Other species such as California lobster, spot prawn, white sea bass, and sea urchins are only fished seasonally to protect specific spawning seasons.