Since the late 1960s, point-sources of water pollution have been reduced due to their ease of identification and treatment. As water quality problems remain and further point-source measures become less cost-effective, attention is directed toward reducing agricultural nonpoint-sources of P and N. In the past, separate strategies for P and N were developed and implemented at farm or watershed scales. Because of differing biology, chemistry, and flow pathways of P and N in soil, these narrowly targeted strategies may lead to mixed results. In some cases, N management of manures has increased soil P and subsequent P enrichment of surface runoff, while no-till has reduced P losses but increased nitrate leaching. Thus, an integrated approach to nutrient management is needed, with best management practices (BMPs) targeted to critical areas of a watershed that contribute most of the P and N exported. We have developed indices that identify critical sources and transport pathways controlling P and N export. These indices are applied to a mixed land use watershed in Pennsylvania. Areas most vulnerable to P loss are limited to small, well-defined areas of the watershed (<20% of area) near the stream channel. In contrast to P, larger areas contribute to nitrate leaching and generally occur on the upper boundaries of the watershed (60%), where freely draining soils and high manure and fertilizer N applications are made. Thus, differing levels of nutrient management may be appropriate for different areas of a watershed.