This is a review of physical, chemical, and biological processes governing microbial transport in the saturated subsurface. We begin with the conceptual models of the biophase that underlie mathematical descriptions of these processes and the physical processes that provide the framework for recent focus on less understood processes. Novel conceptual models of the interactions between cell surface structures and other surfaces are introduced, that are more realistic than the oft-relied upon DLVO theory of colloid stability. Biological processes reviewed include active adhesion/detachment (cell partitioning between aqueous and solid phase initiated by cell metabolism) and chemotaxis (motility in response to chemical gradients). We also discuss mathematical issues involved in upscaling results from the cell scale to the Darcy and field scales. Finally, recent studies at the Oyster, Virginia field site are discussed in terms of relating laboratory results to field scale problems of bioremediation and pathogen transport in the natural subsurface.