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In 1998 the North Bosque River (NBR) was included in the Clean Water Act (CWA) 303(d) List, and assessed as impaired under narrative water quality standards for nutrients and aquatic plant growth. The Texas Institute for Applied Environmental Research (TIAER) used the Soil Water Assessment Tool (SWAT) to develop a soluble reactive phosphorus (P) Total Maximum Daily Load (TMDL) for the NBR. In September 2000, the Texas Commission on Environmental Quality released the TMDL for public review. It was ascertained that additional effort would be needed to address public concerns regarding: 1) lack of spatial resolution in the definition of subbasins; 2) exclusion of the 40 Public Law (PL)-566 flood retardation reservoirs in the watershed; and 3) contributions of discharges associated with dairy lagoons. In addition, improved simulation of in-stream water quality kinetics was pursued to simulate algae growth and nutrient dynamics that have a profound effect on average daily nutrient concentration during low flow. First, the refined SWAT model was calibrated to historical long-term (30-year) base, surface and total streamflow data at three sites along the NBR (goodness-of-fit (NSE) values > 0.70, and percent error < 13.0). The model was then calibrated and verified for monthly streamflow and nutrient loads (NSE > 0.6 and percent error < 15 for streamflow, total nitrogen and total P at major subwatershed outlets) as well as average daily load and concentration using water quality and streamflow data collected by TIAER at over a dozen sites within the NBR watershed during the 1990s.