The diffusive gradients in thin films (DGT) technique has been used for monitoring various organic pollutants in surface water in recent years. This article applies a novel DGT passive sampler to the Nanjing section of the Yangtze River and urban rivers to measure the in-situ concentrations of polycyclic aromatic hydrocarbons (PAHs), analyze their seasonal changes and determine their fate. PAH concentrations had marked seasonality. The concentration of individual PAH was 1.3-18 ng/L in summer and 4.2-161 ng/L in winter. Source inputs, flow differences and degradation/losses caused the seasonal differences. Inputs from Nanjing and tributary rivers were minor compared to the cumulative loads of PAHs in the main Yangtze river upstream of the city. Petrochemical enterprises along the Yangtze River, ship transportation, and upstream pollution were the main sources of pollution in this area. Source analysis indicated a mixed source with coal and biomass combustion inputs increasing significantly in winter. Risk assessment indicated that although the Yangtze River protection policy has reduced pollution in recent years, water quality still exceeded PAH ecological thresholds in the river and the chemical industry cluster areas during winter. Further measures are needed to reduce pollution and its associated risks from a catchment perspective.