This study presents an integrated approach for targeting critical source areas (CSAs) to control nonpoint source pollution in watersheds. CSAs are the intersections between hydrologically sensitive areas (HSAs) and high pollution producing areas of watersheds. HSAs are the areas with high hydrological sensitivity and potential for generating runoff. They were based on a soil topographic index in consistence of a saturation excess runoff process. High pollution producing areas are the areas that have a high potential for generating pollutants. Such areas were based on simulated pollution loads to streams by the Soil and Water Assessment Tool. The integrated approach is applied to the Neshanic River watershed, a suburban watershed with mixed land uses in New Jersey in the U.S. Results show that several land uses result in water pollution: agricultural land causes sediment, nitrogen and phosphorus pollution; wetlands cause sediment and phosphorus pollution; and urban lands cause nitrogen and phosphorus pollution. The primary CSAs are agricultural lands for all three pollutants, urban lands for nitrogen and phosphorus, and wetlands for sediment and phosphorus. Some pollution producing areas were not classified into CSAs because they are not located in HSAs and the pollutants generated in those areas are less likely to be transported by runoff into streams. The integrated approach identifies CSAs at a very fine scale, which is useful for targeting the implementation of best management practices for water quality improvement, and can be applied broadly in different watersheds to improve the economic efficiency of controlling nonpoint source pollution.