Literature on groundwater microbiology is scarce, and even less is known about communities inhabiting aquifers with respect to different host rocks. However, it might be important to consider the geogenic setting in which the groundwater is located, since physicochemical boundary conditions clearly determine the niches for propagation and growth of microorganisms. With temperatures up to somewhere near 150°C, pH ranges from 4 to 9, and strongly varying redox conditions, microorganisms are versatile and may inhabit widely different habitats. Chemolithotrophy and heterotrophic growth with manifold metabolisms allow communities to develop, depending on primary production, completely independent from light. With extensive drilling programs, groundwater aquifer microbiology becomes more and more accessible, and the advent of modern techniques allows determination not only of the microbial diversity, but of their metabolic activity as well. Thus, with this chapter, we want to summarize the state of knowledge on microbial presence and activity with respect to the different geogenic settings in order to provide a better understanding of formation-specific microbiology. Only such a detailed understanding will enable a tailored manipulation of subsurface systems, which seems the only way to address contamination in groundwater and prevent spreading of contaminants. While geological measures address only the water phase, e.g., by pump-and-treat measures, insoluble organic phases are resilient and cannot be treated in an aquifer. With a better understanding of microbiological performance within the aquifer, the in situ treatment might provide future cost-effective, sustainable, ecosystem-friendly ways of remediation. © 2014 Elsevier Inc. All rights reserved.