Urban runoff pollution has become one of the major sources of water pollution. Rapid urbanization process in China has led to a significant increase in the pollution loads, which has posed great threats on the regional water environmental safety. Thus, it is of great importance to systematically analyse the characteristics of runoff pollution in some typical highly urbanized regions. Taking the Dongguan City in South China as the study area, output and spatial characteristics of the pollution emissions were investigated through a GIS-based empirical model. The results showed that the annual pollution loads of chemical oxygen demand (COD), suspended solids (SS), total nitrogen (TN) and total phosphorus (TP) exported from the city were approximately 338489, 613175, 28292 and 2824 t/a, respectively. In particular, the Songshan Lake Area in the city had the largest pollution loads, while the Water Town New Area had the least. In terms of pollution export fluxes unit area, they were highest in the Central Downtown Area (i.e. 2124, 3450, 145 and 16 kg/hm2 a for COD, SS, TN and TP, respectively) and relatively lower in the Southeastern Bordering Shenzhen Area. Enhancing the environmental management and improving the public environmental protection awareness are necessary for mitigating runoff pollution.