Climate change and natural hazards can have detrimental effects on biodiversity and a serious impact on people’s livelihoods and communities. Increased frequency and intensity of extreme weather conditions globally have a major effect on cultural heritage that represents tangible (i.e., monuments, historic buildings and sites, cultural landscapes) and intangible (i.e., knowledge, cultural and social practices, oral traditions) assets that are inherited from the past. Sea level rise, ocean acidification, increased storm intensity, temperature rise, and coastal erosion threaten to adversely impact the stability, preservation, conservation and security of tangible and intangible underwater and coastal cultural heritage. Remote Sensing has proven to be very useful in hazards monitoring and damage assessment of cultural heritage monuments as well as monitoring the effects that result from changes in the broader sites of the monuments. Especially, hyperspectral remote sensing techniques can be used to accurately map efflorescence, daub, salt crystallization, vegetation on building walls, moss, etc. It has been shown that the spectral signatures of various corrosion factors can be extracted using spectral unmixing methodologies. The extracted signatures and corresponding abundance maps can then be linked to the detailed geometry of the cultural heritage buildings, leading to the analysis, mapping and assessment of materials and material deterioration. Even though these methods have been explored on monuments located on land, there has yet to be an attempt to apply them on underwater cultural heritage sites. In this study, hand-held hyperspectral imaging sensors working within the Visible/Near-Infrared (VNIR) region of the electromagnetic spectrum are tested for the first time in combination with a detailed stereomodel, for underwater cultural heritage material identification and degradation.