Increasing pressures from coastal urbanization have created the need for an integrated approach to address the interactions among human activities, taking into account the significance of protecting coastal ecosystems. In this context, a number of policies are promoted at a European, Mediterranean and national level relating to an integrated approach of coastal area management and sustainable development of the urban environment. Among these, Integrated Coastal Zone Management (ICZM) and urban regeneration seem to share common principles and characteristics. Therefore, they constitute the framework within which waterfront development can be approached, namely as part of the urban coast where significant interactions among human activities but also between land and sea uses occur. This paper provides a methodology for the development of a decision making tool (ENCoRe), which is based on multi-criteria analysis and explores local stakeholders' perceptions in terms of priority actions for waterfront development. The tool includes sixteen (16) variables assessing the waterfront and providing the main priorities for waterfront regeneration while it is implemented in four Greek medium-sized coastal cities: Volos, Heraklion, Kavala and Patras. The results highlight four important fields of intervention: management and protection of the environment, spatial adaptability, accessibility and connectivity. The tool can be adapted in other cases providing an opportunity for comparative analysis among coastal cities, highlighting similarities and differences among waterfronts and providing a list of prioritized fields of intervention for waterfront regeneration in the context of ICZM.