This study examines the impact of climate change on the archaeological heritage of Motya, an ancient Phoenician settlement located in Sicily’s Marsala Lagoon. The research highlights the vulnerability of coastal archaeological sites to rising sea levels, tidal oscillations, and wind erosion. Employing advanced technologies, including photogrammetry, UAV surveys, and GIS-based analyses, the study documents historical and current degradation patterns, offering detailed projections for the future. Particular attention is given to the Kothon, Tophet, and North Gate areas, which face significant threats from erosion and submersion. Strategies for preservation include naturalistic engineering solutions, such as re-planting coastal dunes and implementing protective barriers, alongside innovative techniques like virtual restoration and 3D modeling. These approaches not only safeguard the site but also enhance its accessibility and integration into the broader Mediterranean landscape. The findings emphasize the need for integrated management strategies to mitigate the effects of climate change while maintaining the cultural and environmental significance of this unique archaeological context.