This paper presents the nanoindentation investigation of the evolution of concrete microstructure modified by the Internal Crystallization Technology mineral powders. The samples under study were retrieved from a fragment of a circular concrete lining of the vertical mine shaft at a depth of approximately 1,000 m. Due to the aggressive environment and exposure to contaminated water, the internal surface of the structure was deteriorated, decreasing its strength significantly. The mineral powders were applied directly on the surface lining. The specimens were investigated one month, three months and one year after the application of the aforementioned substance in order to verify the time dependence of the strengthening processes and durability of the crystalline phase. The microstructural changes of concrete were assessed with the use of nanoindentation technique. The testing procedure involved including the previously cut specimens in the epoxy resin and grinding and polishing in order to reduce the surface roughness. As a result of the nanoindentation tests the hardness as well as Young’s modulus of the material were evaluated. The results were then compared and statistically analyzed. As a consequence, the disintegration time of the crystalline network in the pores of concrete was identified.