Shallow-water cultural heritage occupies a dynamic land-sea interface where coastal erosion, sediment transport, limited visibility and burial processes hinder conventional archaeological investigation. This paper presents an integrated geoinformatics framework for reconstructing the cultural dynamics of coastal and shallow submerged archaeological landscapes in southeastern Crete, Greece. The methodology combines multispectral remote sensing, satellite-derived and in situ bathymetry, UAV and shallow-water photogrammetry, marine geophysics, GIS-based coastal vulnerability, fuzzy logic multi-criteria risk assessment and digital dissemination through augmented reality. The workflow was applied at five representative case studies, including Stomio, Ierapetra harbour, Koufonisi, Chryse and associated coastal sectors. Optical data from Pleiades-1A, PlanetScope, and Sentinel-2A were used for shoreline mapping, feature enhancement, and satellite-derived bathymetry. Geophysical and bathymetric surveys covered more the 4.5 and 10 hectares respectively. UAV photogrammetry produced high resolution orthomosaics, while the proposed experimental Remote Control (RC) boat extends documentation potential to very shallow submerged environments. Integrated interpretation clarified palaeo-shorelines, submerged harbour structures, fish tanks, architectural continuities and archaeological risk hotspots. The results demonstrate a scalable and transferable framework for documenting, interpreting, monitoring, and communicating endangered shallow-water cultural landscapes.