Microbial corrosion of waterproof coatings causes structural damage to buildings and renovation materials and severely threatens human health. In practical applications, coatings with different base materials show different durabilities to external environmental influences. There is little literature on the antimicrobial durability performance of waterproof coatings. Therefore, this paper selected four standard waterproofing coatings, including polyurethane coatings, cement-based coatings, asphalt-modified polymer coatings, and polymer emulsion coatings, as the main body of this study. Their antimicrobial abilities against Gram-negative Escherichia coli, Gram-positive Staphylococcus aureus, Candida albicans, and mold were tested after experiencing three kinds of harsh environments: Ultraviolet ray (UV), water immersion, and low temperature. The results show that the extreme climates significantly reduced the ability of the four coatings to resist mold, and the highest growth rate of bacteria was 54.64%. Under UV conditions, the polymer emulsion coatings were significantly more resistant to Candida albicans, and the optical density of the bacterial liquid showed a negative growth trend. The microstructural integrity of the polymer emulsion coatings was found to be damaged by Scanning Electron Microscope (SEM) observation. This work improves the durability application research on these coatings and provides a valuable reference for developing new environmentally friendly, antibacterial, and anticorrosive waterproof coatings.