This study presents the development of a vulnerability assessment methodology combining both hydraulic and oceanographic values to evaluate the fragility of the island’s coast, subject to floods. The study area covers the coastal part Petra - Molyvos in North-West Lesvos Island, Greece. Petra stream drains a catchment area of 8.06 km². The flooded sections of the river’s coastal part are analyzed by the HEC-RAS model, while the coastal vulnerability index (CVI) was calculated by the InVEST model. The scenario of habitats’ role in beach protection showed 53% of coastal protection and the CVI moderate exposure to sandy beaches. A change in the geomorphology of the estuary was observed during the summer period, due to the river sediment dredging and small delta reclamation processes.