Phosphorus sources within the Graywood Gully watershed impact water quality within the stream and receiving waters of Conesus Lake, New York. A mass balance approach was instructive in demonstrating the semi-quantitative impact of nonpoint and point nutrient sources on downstream aquatic systems and provided a mechanism to assist in targeting and prioritizing structural best management practices (BMPs) for agricultural areas. The identification and quantification of these sources reveal substantial sources coming from outside the topographic watershed boundary due to the overprint of the built environment on natural surface runoff pathways. The analysis of water sources and phosphorus loading indicated the importance of critical source areas in the watershed and adjacent areas and the effect of the built environment, including drain systems and road ditches, on changing critical hydrological pathways. The impact of BMPs within the watershed was masked by the external contributions from the “extended” watershed, adding over 40% of the total P load to Conesus Lake. This result suggests that the lack of significant decrease in dissolved phosphorus observed in the heavily managed Graywood sub-watershed is a result of not considering the “extended” watershed.