The distribution and fate of chlorinated pesticides, biomarkers, and polycyclic aromatic hydrocarbons (PAHs) in surficial sediments along a contamination gradient in the Lauritzen Canal and Richmond Harbor in San Francisco Bay was investigated. Compounds were identified and quantified using gas chromatography-ion trap mass spectrometry. Biomarkers and PAHs were derived primarily from weathered petroleum. DDT was reductively dechlorinated under anoxic conditions to DDD and several minor degradation products, DDMU, DDMS, and DDNU. Under aerobic conditions, DDT was dehydrochlorinated to DDE and DBP. Aerobic degradation of DDT was diminished or inhibited in zones of high concentration, and increased significantly in zones of lower concentration: Other chlorinated pesticides identified in sediment included dieldrin and chlordane isomers. Multivariate analysis of the distributions of the DDTs suggested that there are probably two sources of DDD. In addition, DDE and DDMU are probably formed by similar mechanisms, i.e. dehydrochlorination. A steep concentration gradient existed from the Canal to the Outer Richmond Harbor, but higher levels of DDD than those found in the remainder of the Bay indicated that these contaminants are transported on particulates and colloidal organic matter from this source into San Francisco Bay. Chlorinated pesticides and PAHs may pose a potential problem to biota in San Francisco Bay.