The objective of this research was to develop a relational database management system(RDBMS) to collect, manage and analyze data on agricultural non-point source(NPS) pollution. The system consists of the relational database for agricultural NPS data and data process modules. The data process modules were composed of four sub-modules for data input, management, analysis, and output. The data collected from the watershed of the upper Cheongmi stream and Geunsam-Ri were used in this study. The database was constructed using Apache Derby with meteorological, hydrological, water quality, and soil characteristics. Agricultural NPS-Data Management System(ANPS-DMS) was developed using Oracle Java. The system developed in this study can deal with a variety of agricultural NPS data and is expected to provide an appropriate data management tool for agricultural NPS studies.