Stable and long-term operation of buried foundations, tunnels, and underground structures requires maximum protection against groundwater exposure. Current waterproofing methods are quite effective for protecting subterranean spaces from flooding and concrete structure degradation. However, 95% of newly constructed facilities experience issues related to waterproofing system failures. The development and implementation of new waterproofing technologies, digital monitoring systems, and early warning systems for waterproofing integrity breaches represent a critical task for the construction and manufacturing sectors thereby demanding advancement and refinement of relevant research methodologies. The research objective of this paper is to develop a methodology for selecting optimal waterproofing solutions for underground part of a building. The key research outcome is the development of an algorithm for finding optimal waterproofing module-based solutions for underground part of buildings. This methodology enables evidence-based selection of the most effective waterproofing installation or repair technology for current underground structures, accounting for diverse design stage conditions. The developed methodology comprises three modules for selecting design solutions: economic impact assessment comparing initial waterproofing system installation costs with future repair expenditures; classification of site geological conditions and operational environment factors; evaluation of installation timelines and projected repair intervals during the building's service life. The proposed methodology may be treated as a conceptual framework for advancing quality assessment criteria—specifically, by augmenting the decision-making toolkit with optimized parameters for selecting future planned waterproofing installation and repair system.