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Water quality modeling and regulatory management guideline study was conducted on a predominantly agricultural 1499-ha (3,700 acres) watershed in the Naval Security Group Activity (NSGA) Northwest base at the States of Virginia/North Carolina border. The watershed has a baseline nonpoint source pollution (NPS) contributing to the Northwest River that eventually influxes to the Chesapeake Bay. Stormwater runoff discharge from the watershed influxes to the Northwest River, approximately 6.44 km (4 miles) upstream of the intake from the City of Chesapeakes potable water supply. A distributed parameter water quality model and Geographic Information System (GIS) framework was implemented to develop a spatiotemporal load allocation (LA) BMP and total maximum daily load (TMDL) estimation to abate the current level of NPS pollution at the same time to preserve the quality of drinking water supply at the Northwest River. A Unix-based Arc/INFO GIS was linked to an event-based, large problem domain distributed parameter water quality model to generate runoff synthesis and subsequent transport of pollutants and sediment from the watershed. This bilateral linkage framework resulted in a powerful, up-to-date tool that would be capable of monitoring and instantaneously visualizing the transport of any pollutant as well as effectively identifying critical areas of the NPS pollution. The framework was also used to simulate various what if scenarios of event-based and background load (BL) of pollutants to develop WLA and TMDL through regulatory best management practice (BMP) protocols. Results showed that the optimal BMP scenario achieved an average reduction of about 41% in soluble and sediment-attached nitrogen and about 62% reduction in soluble and sediment phosphorous from current NPS pollution levels.