Best management practices (BMPs) are increasingly being used by decision makers to reduce agricultural non-point source (NPS) pollution while improving productivity for the farmers. Models are used as planning tools and are especially useful for targeting priority areas for BMP implementation. This study describes a modeling system to assess the impacts of agricultural NPS pollution on coastal environments. The approach is based on Remote Sensing (RS), Geographical Information Systems (GIS) and Hydrological Modeling (HM) and applied to a pilot watershed – catchment area of Nif Creek – in the Aegean region of Turkey. Land Use and Land Cover (LULC) map of the selected area is produced from LANDSAT MSS image based on Co-ordination of Information on the Environment (CORINE) classification scheme. Simulator for Water Resources in Rural Basins (SWRRB-WQ) was used to estimate the NPS pollution loads. The effects of agricultural management practices such as application of irrigation, fertilizer and tillage on the streamflow quality and quantity can be determined by such a modeling system.