In this study, an information system was developed to manage the agricultural non-point source pollution information of Jiulong river watershed, Fujian province, southeast China. The system was developed using Visual Basic programming language, integrated with GIS technology. It was comprised of three modules, the information inquiry module, the AnnAGNPS modeling module and the simulation result demonstration module. All the data in the database come from remote sensing data interpretation, map digitalization, and field investigation. MapObjects is embeded in the program to operate the shapefiles. AnnAGNPS model was used to model the agricultural non-point source pollution. Some scenarios were set to model the different conditions, such as changing the banana field to rice land, removing all the intensive piggeries and so on. Because AnnAGNPS runs in an ArcView window, a special program was developed to make AnnAGNPS run in a Visual Basic MDIchild form. In order to reduce the complexity of the AnnAGNPS-ArcView Interface, it was customized to hold only the necessary menus used in the modeling process. The modeling results were dBASE files, which can be linked to the corresponding shapefiles to visualize the simulation results. User can use the system to identify the critical areas of agricultural on-point source pollution in Jiulong river watershed and compare the results of different scenarios.