Stormwater runoff and associated pollutants from urban areas in the greater Chesapeake Bay Watershed (CBW) impair local streams and downstream ecosystems, despite urbanized land comprising only 7% of the CBW area. More recently, stormwater best management practices (BMPs) have been implemented in a low impact development (LID) manner to treat stormwater runoff closer to its source. This approach included the development of a novel BMP model to compare traditional and LID design, pioneering the use of comprehensively digitized storm sewer infrastructure and BMP design connectivity with spatial patterns in a geographic information system at the watershed scale. The goal was to compare total watershed pollutant removal efficiency in two study watersheds with differing spatial patterns of BMP design (traditional and LID), by quantifying the improved water quality benefit of LID BMP design. An estimate of uncertainty was included in the modeling framework by using ranges for BMP pollutant removal efficiencies that were based on the literature. Our model, using Monte Carlo analysis, predicted that the LID watershed removed approximately 78 kg more nitrogen, 3 kg more phosphorus, and 1,592 kg more sediment per square kilometer as compared with the traditional watershed on an annual basis. Our research provides planners a valuable model to prioritize watersheds for BMP design based on model results or in optimizing BMP selection.