Discharge of olive mill wastewater (OMWW) into rivers system in Crete had led to heavy organic pollution and several drastic environmental impacts. The current research study aims to map and evaluate the environmental hazards initiated by olive mill wastewater pollution discharged into surface stream network of Kolymvari agricultural area located in western Crete, Greece. Implemented methodology is based on locating source points of pollution and determining pollutant surface flow paths under GIS environment. Hydrological features of the area were delineated in the GIS environment using basically elevation data provided by the Ministry of Agriculture. On a microscale, it was proved that the implementation of MCA can quantify the environmental risk to surface water resources caused by OMWW. On a macroscale, risk mapping was implemented by establishing a spatial connection between the source points of pollution and the possible sedimentation areas. Furthermore, mapping of olive mill waste tanks will positively improve the exercised methodology in term of assessing the potential risks of soil and groundwater pollution.