Abstract Microorganisms are implicated in a wide array of geochemical processes of importance to the clay sciences; a point that is highlighted in special issues of journals such asGeochimica et Cosmochimica Acta(2004, Vol. 68, no. 15) andClays and Clay Minerals(2005, Vol. 53, no 6). Life and geochemistry often overlap at the micron scale; i.e., that of a clay mineral, as organisms seek energy and substrates on which to exist and grow. Organisms can only work within the realm of thermodynamic reality. However, as is becoming increasingly evident, the ability of microorganisms to affect fundamental parameters such as pH and redox potential and to strongly affect reaction kinetics can be tied to ecological factors, most likely involving complex feedback. Studies of microbial-mineral-metal interactions have provided substantive evidence for the role of microorganisms in shaping metal fate and transport (Islam et al. 2004;Holden and Adams 2003;Ehrlich 2002). As yet, there is no conceptual foundation that links microbial ecology, metabolism and geochemistry; but new tools are emerging that are leading to a more unified model of microbial biogeochemistry, including interactions with clays and clay minerals. This chapter provides a basic framework for investigating biogeochemical processes, and sets the stage for more detailed chapters on Methods for Investigating Microbial-Mineral Interactions. This chapter begins with basic discussion of geomicrobiology with an emphasis on bacteria and mineral (particularly clay) interactions, and ends with a detailed ‘case study’ of a field investigation of geomicrobiologic processes in acid rock drainage.