Nonpoint source pollution (NPSP) is a serious environmental problem faced by megacities throughout the world. Unlike small cities, problems associated with NPSP are more complex in developing megacities. However, long-term spatial and temporal variations in NPSP, as well as the driving forces behind these changes, are still unknown for a developing megacity. In this study, we used a model set containing export coefficients and statistical models to calculate NPSP load for five NPSP types from 2006 to 2016 in Beijing and its four city functional zones. Our results indicate that the total NPSP decreased by 8.1% from 2006 to 2016. Agricultural NPSP was the largest source of NPSP and measured 46.2% in 2016. Agricultural NPSP, livestock NPSP and soil erosion NPSP decreased by 19.1%, 38.7%, and 0.8%. However, urban NPSP and rural NPSP increased by 10.8% and 8.5%. In the four functional zones, urban NPSP in the capital function core zone decreased by 17.3%, total NPSP in the urban functional development zone increased by 43.0%, total NPSP in the urban development fresh zone decreased by 13.1% and total NPSP in the ecological conservation development zone decreased by 14.7%. The urban functional development zone was key to preventing future NPSP.