Twenty quarterly samples were taken of the fish assemblages of San Diego Bay from July 1994 to April 1999. Each quarter, four stations were occupied using a variety of sampling methods (large seine, small seines, square enclosure, purse seine, beam trawl, and otter trawl) designed to assess all components of the ichthyofauna. These samples yielded a total of 497,344 fishes belonging to 78 species and weighing 2,775 kg over the five-year period. Northern anchovy was the most abundant fish species comprising 43% of the total catch despite its virtual absence in 1997-98. followed by topsmelt, the slough anchovy and Pacific sardine. Round stingrays dominated in weight constituting almost 25% of the total biomass taken followed by spotted sand bass, and northern anchovy. Both numerical abundance and biomass were highest in the spring and summer months due largely to heavy recruitment of juvenile surfperches, topsmelt and northern anchovies. Large catches of northern anchovies, Pacific sardines, round stingrays, and spotted sand bass also contributed to the pronounced peaks in most July samples. Approximately 70% of all individual fish captured in San Diego Bay during this study were juveniles. The 40 most common species/recruits clustered into eleven, resident and seasonal groups. According to canonical correlation analysis, distance from the mouth of the bay, depth, temperature, and salinity accounted for nearly 88% (R 2 = 0.875) of the variance in species abundances.