Polychlorinated biphenyls are persistent organic pollutants that are toxic, carcinogenic, and bioaccumulate in organisms. Located in the San Diego Bay are three marinas, Shelter Island Yacht Basin, Harbor Island West, and Harbor Island East. Forty-two surface sediment samples taken from these three marinas during the summer (July) of 2014 were collected to determine the concentration, composition, and spatial distribution of PCBs. The sediment concentrations of 26 PCB congeners were obtained using comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry (GC×GC/ TOF-MS). The mean total PCB concentration for all marinas was 151.7 ng/g dry weight with a standard deviation of 213.4 ng/g. The highest total PCB concentrations occurred in Harbor Island East with a maximum concentration of 1387.2 ng/g. Hotspots were found in Harbor Island East that are adjacent to concrete, soil, storm drains, and old historical sites. PCB congeners 101, 118+123, 138 and 153 were found at 100% frequency of detection. PCB congeners 77, 81, 126, 157, 169, and 189 were non-detects across all sampling sites. PCB 138 and PCB 158 were most abundant, and their average concentrations were 1231.6 and 1131.7 ng/g dry weight. PCB concentrations from the three marinas exceed historical monitoring data that were sampled throughout the San Diego Bay. There were significant median differences between the three marinas. The median concentration of HE and HW were significantly different whereas the median concentration of SIYB and HW were not found to be significantly different. The PCB concentration was highest in Harbor Island East possibly due to historical sources of contamination that includes storm water runoff and old industrial facilities adjacent to the sample sites. Risk assessments from the San Diego Bay indicate that fish consumers are at risk from consumption of fish due to PCB contamination. PAHs, Cu, and PCBs have been found in the three marinas. The toxic risk from the co-occurrence of these chemical remain unknown.