The North Bosque River (NBR) was included in the Clean Water Act § 303(d) impaired list. The Texas Institute for Applied Environmental Research used the Soil Water Assessment Tool (SWAT) to develop a phosphorus (P) Total Maximum Daily Load. SWAT was modified to dynamically change manure application rates based on simulated annual soil P, change areas receiving manure, alter manure quantities each year, apply liquid and solid manure pools separately, move manure between subbasins, improve landscape P processes, model contributions of dairy lagoon discharges and improve in-stream water quality kinetics. Data was refined to increase spatial resolution of subbasins and include Public Law (PL)-566 flood retardation reservoirs. A dual level of model performance was established: one level for large drainage areas and a reduced performance level for all other sites. Main stem sites were to have streamflow, sediment, total nutrients achieve the “good” rating from Moriasi et al. (2007). For secondary sites and constituent parts of total nutrients besides PO4 the “satisfactory” rating was acceptable model performance. This dual level of model performance was developed in recognition of uncertainties in model input and measured data that resulted in better model performance for larger drainage areas as compared to smaller drainage areas, and for total nutrients as opposed to their constituent parts. The refined SWAT model was successfully validated for both historical long-term (30-year) base, surface and total streamflow data and monthly streamflow and nutrient loads , as well as average daily load and concentration using water quality and streamflow data.