Global warming and climate change have destabilized coastal ecosystems, causing flooding and adverse impacts on marine biodiversity. IPCC projections indicate a substantial rise in the global mean sea level, potentially reaching five meters by 2150 in a high-emission scenario. These changes pose significant risks to the geography, urban development, and social structure of coastal Mediterranean communities. European and national policies prioritize strategies to enhance biodiversity through nature-based solutions, aiming to restore natural conditions in urban, degraded, and crucial areas like rivers and coastlines. The contribution, from applied research activities conducted in ABITALab, introduces an innovative protocol structured with adaptive, “green” and ‘grey,” ecological and technological measures, offering effective governance for the “flooding” issue through digital predictive models and interventions applied to the case study of Reggio Calabria’s coastline. The protocol methodology concerns a first phase of coastal climate risk analysis; a second phase of advanced predictive modelling of coastal systems; a third phase of an applicative-planning nature for the definition of actions and sub-actions to address performance levels; and a fourth phase that concerns the implementation of “site-specific” adaptation actions and sub-actions. In the experimental phase, the protocol was tested in coastal areas of Reggio Calabria as a technical and planning support tool in the formulation of local adaptation and resilience strategies for coastal areas subject to the impacts of climate change. The innovation of the protocol is in the use of regenerative digital design to process studies and data, develop predictive models, and visualize meteorological and climatic data. The application considers three periods in the SSP3–7.0 scenario. For each area, a set of solutions is developed according to the structure and the vulnerability of the coast. The protocol integrates adaptation actions into advanced modeling elaborations, in accordance with the Climate Change Adaptation National Plan. These actions include restoring wetlands to improve the coast’s ability to absorb seawater and reduce the risk of flooding, implementing NBS through the restoration of coastal vegetation to protect coasts from erosion, and developing SUDS to reduce the amount of surface water that reaches the coasts. Three potential research developments can be identified: the integration into the local policy framework; the scalability to multiple contexts at the metropolitan, regional, and national levels; and the application of an experimental assessment model based on validated protocols, such as IUCN.