Human activities and specific geological and oceanographic conditions can affect the exposure of small river coastal parts to erosion and flooding. 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 and climate change impact. The study area covers the coastal part from Petra to Molyvos in West–North Lesvos Island, Greece. Petra stream 1.75 km in length drains the catchment area of 7.97 km², with a mean flow of 3.52 m³/s, a mean width of 6.15 m, a mean slope is 1.03% and a mean depth is 1.63 m, and flows into the Aegean Sea. 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 HEC-RAS model estimated the critical cross-sections (CSs) 2 and 3 at the stream mouth are the first to show overflow equal to 8 m³/s reducing the upstream flow which could reach 11m³/s with appropriate riverbed shaping. CS 26 (depth 0.54m and width 4.43m, upstream of the mouth at 650 m) reduces the upstream drainage of the stream and overflow with a flow rate of 1.5 m³/s. While the INVEST computes the CVI by combining the ranks of up to seven ecological and physical variables at each shoreline point. Ranks vary from very low exposure (rank=1) to very high exposure (rank=5), based on a mixture of user- and model-defined criteria. 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. The CVI results are expected to show that 10% of the coastal zone is in high hazard.