Environmental problems arising from non-point source (NPS) pollutants due to intense agricultural activities are constantly increasing and land-based water pollution has continued to be a serious environmental problem in Thachin river basin, Thailand. In this study, a physically based watershed scale hydrologic/water quality model SWAT has been applied to predict the NPS pollutant loadings from the watershed and identify the critical sub-watersheds under threat from NPS pollution as well as simulate different management strategies based on tillage and fertilizer addressing NPS pollution. Consequently, SWAT is found to be a promising tool to predict the NPS pollutant loads from Thachin river basin if satisfactorily calibrated and validated. The adequately calibrated and validated SWAT model could help in tracing critical pollution areas requiring immediate actions for remediation measures and could also serve as a decision making tool for planning and management of watersheds to evaluate the impact of alternative management practices.