Buffer zone selection technique for natural purification of livestock wastewater within a small agricultural watershed was developed using Geographic Information Systems. The technique was applied to 4.12 km2 watershed located in Gosan-myun, Ansung-gun which have 20 livestock farmhouses. As a necessary data for selecting process, feedlot site map, digital Elevation Model (DEM), stream network, soil and land use map were prepared. By using these data, wastewater moving-path tracing program from each feedlot to the stream was developed to get the basic topographic factors; average slope through the paths, distance to the nearest stream and watershed outlet. To identify the vulnerable feedlots for storm event, the grid-based storm runoff model (Kim, 1998; Kim et al., 1998) was adopted. The result helps to narrow down the suitable area of buffer zone, and finally by using subjective but persuasive conditions related to elevation, slope and land use, the suitable buffer zones were selected.