A watershed scale water quality evaluation system was developed for assessing spatial variation of subsurface pesticide movement. The system consists of a linked-transport model component for performing simulation and a GIS component for processing spatially-related data. The surface heterogeneity caused by agricultural activities, topographic, hydrologic, and soil type variations in a watershed was handled by partitioning the watershed into homogeneous subfields. The subsurface soil profile and aquifer heterogeneities were considered by dividing the subsurface domain into root zone, intermediate vadose zone, and saturated zone, respectively. On each of the homogeneous subfields, the physically-based models, PRZM and VADOFT, were linked to simulate pesticide transport in the root and intermediated vadose zones. Pesticide movement in groundwater underneath the watershed was simulated by linking the other two models with SUTRA. An irregular shape finite element mesh generator was developed for fitting the irregular shape watershed boundary and reducing the number of nodes of the finite element mesh. Either transient or steady state flow and transport simulation could be performed with the system. The system is able quantitatively to produce detailed spatial variation maps of pesticide concentrations at any desired depth in the unsaturated zone and in groundwater. The system requires spatially-distributed information as inputs. Management of large volumes of spatially-referenced data which represent the heterogeneous properties of the watershed were facilitated by a developed GIS component. The GIS data processing component was composed of spatial data manipulation and display, attribute database management, and model input information extraction subcomponents. The spatial data processing component consists of data format conversion, map registering, map editing, new information generation, and map display subcomponents. / Ph. D.