Sea level rise is one of the main risk factors for the preservation of cultural heritage sites located along the coasts of the Mediterranean basin. Coastal retreat, erosion, and storm surges are posing serious threats to archaeological and historical structures built along the coastal zones of this region. In order to assess the coastal changes by the end of 2100 under the expected sea level rise of about 1 m, we need a detailed determination of the current coastline position based on high resolution Digital Surface Models (DSM). This paper focuses on the use of very high-resolution Unmanned Aerial Vehicles (UAV) imagery for the generation of ultra-high-resolution mapping of the coastal archaeological area of Pyrgi, Italy, which is located near Rome. The processing of the UAV imagery resulted in the generation of a DSM and an orthophoto with an accuracy of 1.94 cm/pixel. The integration of topographic data with two sea level rise projections in the Intergovernmental Panel on Climate Change (IPCC) AR5 2.6 and 8.5 climatic scenarios for this area of the Mediterranean are used to map sea level rise scenarios for 2050 and 2100. The effects of the Vertical Land Motion (VLM) as estimated from two nearby continuous Global Navigation Satellite System (GNSS) stations located as close as possible to the coastline are included in the analysis. Relative sea level rise projections provide values at 0.30 ± 0.15 cm by 2050 and 0.56 ± 0.22 cm by 2100 for the IPCC AR5 8.5 scenarios and at 0.13 ± 0.05 cm by 2050 and 0.17 ± 0.22 cm by 2100, for the IPCC Fifth Assessment Report (AR5) 2.6 scenario. These values of rise correspond to a potential beach loss between 12.6% and 23.5% in 2100 for Representative Concentration Pathway (RCP) 2.6 and 8.5 scenarios, respectively, while, during the highest tides, the beach will be provisionally reduced by up to 46.4%. In higher sea level positions and storm surge conditions, the expected maximum wave run up for return time of 1 and 100 years is at 3.37 m and 5.76 m, respectively, which is capable to exceed the local dune system. With these sea level rise scenarios, Pyrgi with its nearby Etruscan temples and the medieval castle of Santa Severa will be exposed to high risk of marine flooding, especially during storm surges. Our scenarios show that suitable adaptation and protection strategies are required.