Despite the many strides made in the past two decades, nonpoint source (NPS) pollution continues to be an important environment management and water quality management problem. For the most part, analysis of NPS pollution in watersheds has depended on the use of lumped mathematical models to identify potential problem areas and to assess the effectiveness of alternative management practices. To effectively use models to analyze NPS pollution at the watershed-scale, resource managers and researchers have depended on the geographic information system (GIS) technology to determine input parameters and display output from models. There have also been numerous attempts to link GIS with lumped models to extend both the scope and scale of the analysis. The primary goal of this research is to use GIS to facilitate the analysis of water quality problems. A number of integrated modeling environments were developed either by tightly coupling models with GIS or embedding the entire modeling equations inside the GIS, taking advantage of the high-level data structure of the GIS. In one modeling environment, an interactive user interface was developed by tightly coupling the Agricultural Nonpoint Source Pollution model (AGNPS) with ARC/INFO GIS. In another, an interactive water quality modeling environment which incorporated and embed several physical-base/process-base equations for simulating NPS pollution within ARC/INFO GIS was developed. Compared with traditional methods of watershed water quality modeling, the unique GIS modeling environment is far more efficient, saves time, and significantly reduces the tedious task of watershed analysis of nonpoint source pollution.