Greece is a country with a unique morphology. Having an extensive coastline and thousands of islands, the rise of the touristic industry is significant. The recent economic crisis as well as the increased infrastructure construction costs on the islands, created the urge to develop alternative and innovative transport systems. The seaplane, a modern, eco-friendly mode, allows effortless and quick connection between ports and airports from all over the country and distant coastal areas and islands. Seaplanes can be used by both residents and visitors or/and carry shipments. The research presented herein focuses on the development of a methodological framework for the evaluation of different areas for water aerodrome allocation, initially among different islands. Multicriteria decision analysis (MCDA) was selected among the large spectrum of existing evaluation methods, because it was considered to be the most suitable approach as it gives the opportunity to use diverse criteria, both quantitative and qualitative. Significant criteria include the distance between the origin waterdrome location and protected natural areas, wave and wind data of each area, the operational cost of seaplanes and the number of passenger arrivals and departures. Weights are accorded to the criteria based on experts' opinion and applying goal programming approach. The evaluation of the alternatives takes place with the aid of the PROMETHEE method. The suggested approach is then implemented through a case study; the investigation of the potential connection of Thessaloniki, the second-largest city in Greece and a transportation hub for the southeastern Europe and the Balkans, with the Cyclades islands, in South Aegean Region.