Urban non-point source pollution is becoming a serious issue under the context of rapid urbanization and its impacts on surface hydrologic processes. The identification of non-point source risk areas and the effectiveness of source-control measures provides important first steps to improve the degrading aquatic environment but is challenged by the complex dynamics and variabilities of surface pollutants in urban environments. In this study, we investigate the spatial and temporal variabilities of non-point source pollution in a small urban catchment based on numerical simulations and in-situ samplings. Our results show that residential, industrial, and commercial land contribute to the most pollutant loadings and are the main constituents of the pollution risk area. Rainfall duration and intensity are the main factors in determining the temporal variations of urban non-point source pollution. There is no correlation between early drought days and pollution load. Numerical simulations show that it is more effective to increase urban vegetation coverage than to enhance road cleaning for effective non-surface pollution control. For enhanced road cleaning, it is more effective to improve the frequency of road cleaning than its efficiency. Our results provide important guidance for effective controls of non-point source pollution as well as the establishment of long-term surface pollutant monitoring network in complex urban environments.