Residues, potential sources and ecotoxicological effects of polychlorinated biphenyls (PCBs) and organochlorine pesticides (OCPs) were analyzed in typical urban river networks of Shanghai. In total, 47 surface sediments were collected in each of the sampling seasons (summer and winter). Laboratory analysis by GC-ECD showed that OCPs and PCBs concentrations were in medium levels compared to other national and international areas. As for OCP compounds, HCHs and DDTs were two dominant pollutants, with ∑HCHs concentrations ranging from 1.74 to 28.78 ng/g and ∑DDTs concentrations ranging from 0.88 to 25.45 ng/g. For individual HCHs, β-HCH was the most dominant HCH compound, with a mean value of 5.06 ng/g, followed by α-HCH (3.50 ng/g) in winter. A similar case of HCHs was also found in the summer season. Concentrations of ∑18PCBs varied from 6.67 to 37.10 ng/g in winter and from 10.63 to 45.55 ng/g in summer. Individual PCB 28, 101, 118 and 123 were dominant among all congeners, with averages of 3.16, 1.55, 2.47 and 2.37 ng/g in winter, 3.11, 2.34, 4.92 and 4.41 ng/g in summer, respectively. ∑20OCPs (the sum of twenty OCPs) concentrations in cultivated land areas were more abundant than that in artificial surface areas, indicating an abundance of pesticides and fertilizers in cultivated lands. Analysis of possible sources indicated that both industrial and agricultural residues contributed to higher HCHs and DDTs concentrations, which mainly originated from weathered pesticides with aerobic transformation processes. For PCB compounds, a significant seasonal variation, atmospheric precipitation, and surface runoff were the major factors for fluctuated PCBs concentrations. Ecotoxicological assessment based on established sediment quality guidelines (SQGs) showed that DDT compounds have a potential threat to the aquatic environment of our study area.