This paper presents a methodological framework for evaluating marine areas in Greece for the purpose of identifying the most adequate sites for Hybrid Offshore Wind and Wave Energy Systems (HOWiWaES), with special focus on the HOWiWaES’ environmental impact assessment evaluation. Nine evaluation criteria that reflect various environmental, economic, technical and socio-political aspects are considered, including Wind Velocity (WV), Wave Energy Potential (WEP), Water Depth (WD), Distance from Shore (DS), Connection to Local Electrical Grid (CLEG), Population Served (PS), Shipping Density (SD), Distance from Ports (DP) and Environmental Performance Value (EPV). Analytical Hierarchy Process (AHP) is performed to hierarchically rank twelve predefined siting alternatives. Questionnaires are used to collect information on pairwise comparisons of the evaluation criteria from a group of stakeholders/experts. Geographic Information Systems (GIS) are used as a metric tool for pairwise comparisons of each siting alternative with respect to the first eight evaluation criteria, while the last criterion is assessed through the development of an innovative environmental impact assessment tool. The results indicate that WV, WEP and EPV present the evaluation criteria with the highest relative significance, while PS, DP and SD correspond to less influencing criteria. The proposed methodology can be easily applied to other countries worldwide for supporting socially accepted siting of HOWiWaES.