This paper reviews methods for modeling coupled microbial and transport processes in variably saturated porous media. Of special interest in this work are interactions between active microbial growth and other transport processes such as gas diffusion and interphase exchange of O2 and other constituents that partition between the aqueous and gas phases. The role of gas–liquid interfaces on microbial transport is also discussed, and various possible kinetic and equilibrium formulations for bacterial cell attachment and detachment are reviewed. The primary objective of this paper is to highlight areas in which additional research may be needed—both experimental and numerical—to elucidate mechanisms associated with the complex interactions that take place between microbial processes and flow and transport processes in soils. In addition to their general ecological significance, these interactions have global-scale implications for C cycling in the environment and the related issue of climate change.