The only example and reference of Ptolemaic Alexandrian tombs, with clear integrations of Egyptian-style scenes and decorations, is considered an endangered archaeological site due to different coastal environmental risks in Alexandria and the absence of maintenance. Anfushi’s Necropolis is located near the western harbour (Island of Pharos) and dates back to the 2nd century BC. Sea level rises, earthquakes, flooding, storminess, variations in temperature, rainfall, and wind are the factors that have the largest effect on the destruction and decay of Anfushi’s Necropolis building materials. This paper’s main objectives were to characterize this necropolis’s building materials and assess its durability problems and risks regarding the coastal environment. Additionally, the vector mapping of its architectural and structural elements was applied for documentation and recording purposes for the necropolis. To achieve these aims, field (recording and photographs), desk (engineering drawing and mapping), and laboratory works (X-ray diffraction, X-ray fluorescence, binocular microscopy, polarizing microscopy, and scanning electron microscopy) were carried out. The results confirmed the probabilistic risk of sea level rises and its impact on the submergence of Anfushi’s Necropolis. The structural deficiencies of the tombs were caused by the effect of earthquake tremors along with anthropogenic factors. In addition, chemical and microscopic investigations showed that salt weathering (halite and gypsum) induced the decay of the building materials.