Crete, an island rich in coastal cultural heritage, is witnessing the increasing impacts of climate change, with its renowned archaeological sites facing significant threats from sea level rise, coastal erosion, and extreme weather events. This study focuses on a vulnerability assessment of these sites, integrating geospatial technologies to develop an understanding of the risks posed by environmental changes. Employing high-resolution satellite imagery and GIS-based techniques, the research maps out key archaeological sites along Crete’s diverse coastline, which stretches over 1,040 km and features a complex mosaic of geomorphic structures prone to dynamic climatic interactions. The methodology involves a multi-tiered approach, incorporating physical vulnerability indices to assess the threats to cultural heritage. This includes evaluating factors such as proximity to the shoreline, historical erosion rates, current conservation status, and potential socio-economic impacts on tourism, which is vital for the local economy. The study identifies several high-risk areas, notably Kommos, Malia, and Falasarna, where significant archaeological remains are at increased risk of degradation or loss. The findings underscore the urgent need for targeted conservation strategies that are informed by comprehensive risk assessments. By integrating cultural heritage into coastal vulnerability analyses, the study provides crucial insights for policymakers and conservationists, aiming to enhance resilience and preserve Crete’s invaluable archaeological legacy for future generations.