Mathematical models of agricultural runoff processes are being used to analyze and predict the quantity and quality of runoff from agricultural lands. The goal is to use these models to develop a Best Management Practice (BMP) Plan that will maintain agricultural productivity while minimizing adverse water quality impacts. This report describes a basin-scale model application that combines the detailed simulation of agricultural runoff and soil processes, which calculates surface and subsurface pollutant transport to receiving waters, with subsequent simulation of instream transport and transformations. The result is a comprehensive simulation of river basin water quality. Comparison of water quality resulting from conventional agronomic practices and BMPs provides the basis for determining the net effects and associated benefits of BMP implementation.