A number of countries are actively working toward the siting and development of deep geological repositories (DGR) for used nuclear fuel. Given their ubiquity and metabolic capabilities, it is assumed that with sufficient time and appropriate conditions, microorganisms could alter the geochemistry of the repository. As such, the DGR concept provides an invaluable opportunity to evaluate the evolution of subsurface conditions from “disturbance” back to original state. The design concept involves the use of steel or copper/steel used fuel containers, surrounded by a low-permeability, swelling clay buffer material within a low-permeability, stable host rock environment. Within a newly constructed DGR, conditions would be warm, oxidizing, and dry. With sufficient time, these conditions would gradually revert to the original state of the surrounding geology. This chapter discusses how microbes and their metabolic activity may change over time and discusses the potential effects they may have on the engineered barrier system (EBS) that serves to isolate the used fuel containers and on the used fuel itself. The widespread support for the development of underground facilities as a means to ensure safe, long-term storage of increasing inventory of nuclear waste underscores the pressing need to learn more about the impacts of microbial activity on the performance of such facilities over the long term.