The composition, structure, physical, physical-chemical, and mechanical properties of blue Lower Cambrian clays in the western part of the Leningrad Oblast have been analyzed. The blue clay formation is considered as a medium for the disposal of radioactive waste near the Koporje settlement. Complex analysis and assessment of the conditions of formation and transformation of blue clays under the influence of natural and anthropogenic factors has shown that prolonged radioactive irradiation of clay strata leads to an increase in the disintegration of clays, reduces the resistance to shear and deformation properties indicators of the activation of microbiological activity, which are considered as a negative factor. Changes in clay properties contribute to the disturbance of hydrodynamic conditions and increase the risk of aquifer pollution. Nine criteria for safe operation of underground storage facilities based on the study of engineering-geological and geo-environmental factors are proposed. Long-term safety of operation of underground storage facilities in clay strata should be based on the multi-barrier concept of environmental protection.