The establishment of numeric nutrient criteria for the Great Bay Estuary System (GBES) to improve water quality used a computer modeling approach to determine how much of the waste water treatment facility (WWTF) discharges were responsible for nitrogen entering GBES. The Great Bay Estuary, located in southeastern New Hampshire, is a relatively shallow (a tidal amplitude to mean depth ratio of 0.18), well-mixed tidal estuary with a wet area of and a main channel length of approximately 26 km. The dominant tide is the principal lunar (M2). The modeling approach includes both a finite element, two-dimensional, vertically averaged, time stepping circulation model, and a Lagrangian particle tracking module. The spatial discretization uses finite element triangles with a characteristic length ( where A is the triangle area) of roughly 3 m in the estuary. The time discretization uses a time step of 99.36 s. The particle model does not include vertical motion, and the particles are neutrally buoyant passive particles. Several WWTF discharges were selected and run separately as a continuous release of conservative particles. The percentages of particles residing in each region at the end of the simulation time (65 days) from each source were summarized to allow comparison. In addition, the percentage of particles scaled by the total nitrogen load from all WWTFs was also summarized for each region. It was thus possible to assess the relative contribution of each of the selected WWTF modeled made to each region.