Low and intermediate level radioactive waste produced during the operation and decommissioning of nuclear power plants is disposed of in an underground geological repository. The majority of metallic waste is made of various stainless-steels and carbon steel. Microbial communities and groundwater composition in deep bedrock at repository sites were believed to stay stable over time, allowing the prediction of evolution of the repository environment. However, a two-year survey of chemical components and microbial community composition within deep bedrock revealed changes in both. An in situ corrosion monitoring system was developed to monitor real-time corrosion rates of two stainless-steel grades (AISI 304 and 316) to study the evolution of corrosion, and correlation between environmental changes and corrosion rate. Surprisingly, higher corrosion rates of steel coupons were detected in the higher alloyed stainless-steel grade 316 compared to the lower alloyed grade 304. Pitting was the main corrosion form. Sulphate reducing bacteria and methanogenic archaea were enriched on surfaces of both types of steel coupons. These microbes likely have a role in the corrosion of stainless-steel in this environment. The changes in groundwater conditions and microbial communities within deep bedrock groundwater at this repository site may have implications for the nuclide release and transport of radioactive material and the long-term evolution and safety of this repository and continental repositories in general and thus needs to be thoroughly understood.