Abstract In Taiwan, non-point source (NPS) pollution is one of the major causes of the impairment of surface waters. The Kaoping River Basin is the largest and the most intensively used river basin in Taiwan. In the Kaoping River Basin, most of the upper catchment is used for agricultural activities including cropland and livestock farming. In this study, I-Liao Creek watershed, one the major sub-basin of Kaoping River Basin, was selected to study the impact of NPS pollution on river water quality. An integrated watershed management model was applied to investigate potential NPS pollution management plans in the I-Liao Creek watershed. Based on the results from the field investigation and model simulation, the overall ammonia-nitrogen loading to the I-Liao Creek watershed was approximately 92,117 kg/year. The following remedial strategies have been taken to reduce the impacts of NPS pollution on the water quality of Kaoping River and I-Liao Creek: application of best management practice for NPS pollutant control; application of natural treatment systems for stormwater runoff treatment; and construction of the watershed geographical information system (GIS) and real time water quality monitoring system to effectively manage the watershed. Linking land utilization information with the NPS pollution simulation model may further provide essential information of pollution potential of NPS pollution for all sub-regions in the river basin. Experience obtained from this study will be helpful in designing the watershed management and pollution control strategies for other similar river basins.