As a major pollutant source to urban receiving waters, the non-point source pollution from urban runoff needs to be well studied and effectively controlled. Based on monitoring data from urban runoff pollutant sources, this article describes a systematic estimation of total pollutant loads from the urban areas of Beijing. A numerical model was developed to quantify main pollutant loads of urban runoff in Beijing. A sub-procedure is involved in this method, in which the flush process influences both the quantity and quality of stormwater runoff. A statistics-based method was applied in computing the annual pollutant load as an output of the runoff. The proportions of pollutant from point-source and non-point sources were compared. This provides a scientific basis for proper environmental input assessment of urban stormwater pollution to receiving waters, improvement of infrastructure performance, implementation of urban stormwater management, and utilization of stormwater.