Chemical pollution at sites in or near San Diego Bay was investigated between 1984 and 1988. The mean concentrations of selected polychlorinated biphenyls (PCBs), metals (e.g., copper and lead), and aromatic hydrocarbons in sediments from sites in the southern and central portions of the bay were significantly higher (p less-than-or-equal-to 0.05) than those in sediment samples from nearby nonurban sites. Mean concentrations of PCBs in liver tissue and of selected aromatic compounds (e.g., aromatic hydrocarbons) and their metabolites in bile were also significantly higher in white croaker (Genyonemus lineatus), barred sand bass (Paralabrax nebulifer), and black croaker (Cheilotrema saturnum) from one or more sites within the bay compared to those from the nonurban sites. In addition, prevalences of fin erosion in white croaker, barred sand bass, and black croaker and of liver neoplasms in black croaker from sites in the bay were significantly higher than in individuals of the same species from nonurban sites.