Within the SMRMA, fishing or taking any living marine resources is prohibited with the exception that, with a valid state water bottom lease and permit, the recreational taking of finfish and the aquaculture of oysters is permitted north of latitude 35° 19.70′ N. Recreational hunting of waterfowl is allowed unless otherwise restricted by hunting regulations.

Morro Bay serves as an important resting and foraging ground for migratory birds using the Pacific Flyway.

Similar studies in marine protected areas located off of the Santa Barbara Channel Islands have already detected gradual improvements in fish size and number.

[5] Local scientific and educational institutions involved in the monitoring include Stanford University's Hopkins Marine Station, University of California Santa Cruz, Moss Landing Marine Laboratories and Cal Poly San Luis Obispo.

Research methods include hook-and-line sampling, intertidal and scuba diver surveys, and the use of remote operated vehicle (ROV) submarines.