Nonpoint source (NPS), common in agriculture, reaches the environment as runoff from a field, not output from a waste pipe. Its control and regulation are also different from other types of pollution that may seem more familiar.

In 1997, New York City adopted a mammoth watershed agreement to protect its drinking water and avoid filtration of its large upstate surface water supply. Shortly thereafter, the NRC began an analysis of the agreement's scientific validity. The resulting book finds New York City's watershed agreement to be a good template for proactive watershed management that, if properly implemented, will maintain high water quality. However, it cautions that the agreement is not a guarantee of permanent filtration avoidance because of changing regulations, uncertainties regarding pollution sources, advances in treatment technologies, and natural variations in watershed conditions. The book recommends that New York City place its highest priority on pathogenic microorganisms in the watershed and direct its resources toward improving methods for detecting pathogens, understanding pathogen transport and fate, and demonstrating that best management practices will remove pathogens. Other recommendations, which are broadly applicable to surface water supplies across the country, target buffer zones, stormwater management, water quality monitoring, and effluent trading.