Due to limits on available data, the effects of urban sprawl on regional nonpoint source pollution (NPS) have not been investigated over long time periods. In this paper, the characteristics of urban sprawl from 1999 to 2014 in Beijing were explored by analyzing historical land-use data. The Event Mean Concentration data have been collected from all available references, which were used to estimate the variation in urban NPSs. Moreover, the impacts of variation in urban sprawl on regional NPSs were qualified. The results indicated that the urbanization process showed different influences on pollutants, while COD and TN were identified as key NPS pollutants. Residential areas contributed more NPS pollutants than did roads, which played a tremendous role in the control of urban NPS. The results also suggested in part that the impact of urban sprawl on the variation of COD decreased while TN increased in Beijing during the study period. These results would provide insight into the impacts of urban sprawl on NPS variation over a long period, as well as the reference for reasonable urban planning directives.