Long-term operation in difficult engineering-geological conditions of unique underground sewage facilities creates the danger of violating their structural safety. A long-term study of the dynamics of changes in a technical state of large pumping stations and deep sewage tunnels made it possible to establish patterns of influence of intensive anthropogenic and dynamic actions on this process. The developed discrete and continuous diagnostic models of defect development in tunnel structures allow identifying potentially hazardous areas subjected to manifestation of critical failures and methods of their localization. On the basis of numerical modeling the boundaries of defect-free joint operation of the system “source of impact – geo-mass – sewage underground structure” have been determined. The geotechnical and structural calculations are used to simulate the interaction of the facilities with the soil environment and predict adaptive stress-strain control system parameters. With increasing external anthropogenic and dynamic impacts, modeling zones of urban areas with potentially dangerous sections of underground sewage facilities constitute the basis for development of regulatory documents on monitoring methods and safe development of the geotechnical infrastructure of a megacity.