Water resources are subjected to different pollution sources. Point source water pollution of surface water is an important issue when considering the limited surface water availability as well as the potential knock-on effects of this pollution on human health as well as habitat and land degradation. One of the main point sources of water pollution is Olive Mill Waste Water (OMWW). OMWW is the liquid by-product generated during olive oil production. However, there is no standardized method to assess the risk of water pollution by OMWW for any given river basin. This research addressed the above issue by designing a detailed quantitative risk assessment methodology, which utilizes Geographic Information System (GIS) modeling to classify within a watershed individual sub-catchment risk of water pollution occurring from olive mill waste discharges. The research presents the proposed criteria and calculations required to estimate sub-catchment risk significance and comments on the potential of the method for wider application. This research combines elements from risk assessment frameworks, Multi-Criteria Analysis (MCA), and GIS. MCA helped in aggregating different aspects and elements associated with this environmental problem, while GIS modeling tools helped in obtaining many criterion values and providing insight into how different objects interact in nature and how these interactions influence risk at the watershed level. The proposed method was tested in the Keritis watershed in Crete, Greece, where OMWW is one of the main stressors influencing water quality, and the results indicated that this method has the potential to be a useful guide to prioritize risk management actions and mitigation measures to be incorporated in River Basin Management Plans.