Semi-enclosed bays are used for critical economic activities such as ports, aquaculture, and human settlement due to their topography and ocean connectivity. However, the role of these geomorphological characteristics on the accumulation of chlorinated organic pollutants in semi-enclosed bays is poorly understood. We investigated the spatiotemporal distribution and potential ecological risk of organochlorine pesticides (OCPs) and polychlorinated biphenyls (PCBs) in sediments from Shantou Bay, a semi-enclosed bay. The ∑PCB concentration was 258–1297 ng g−1 and 59.6–651 ng g−1 in the dry season and wet season, respectively. Sediments collected downstream and upstream the aquaculture farms had significantly lower DDT concentrations than those collected close to the aquaculture discharge points. The ratio of DDT and its metabolites indicated that there was possible fresh input of DDTs into Shantou Bay. However, no significant spatial trend was observed in the PCB profiles. The concentrations of PCBs and OCPs in Shantou Bay were above the China Marine Sediment Quality Class I suggesting remediation was essential to ensure the aquatic systems could be safely used for fisheries, swimming, or as marine protected areas. Furthermore, the potential ecological risk of DDTs was high as it exceeded the effects thresholds at all sites. Seasonal variations in human activities, resuspension of historical contaminants due to physical oceanographic, climatic and hydrological factors, and contaminant trapping probably contributed to the changes in organic pollutant distribution in the semi-enclosed bay.