Abstract Bioremediation of contaminated soils by pumping-in beneficial microorganisms to degrade and eventually remove undesirable organic pollutants is gaining popularity for soil treatment. One critical step of bioremediation involves introducing beneficial microbes, such as bacteria and fungi, into soils to break down contaminants as the microbes carry out their life functions. The current state of knowledge on this subject has been built primarily on experimental work, and the development of a numerical method that is capable of accurately analyzing and predicting bacterial propagation in variably saturated soils has not been adequately explored. Within this background, this article presents the development of a finite element method (FEM)-based model for determining the mobility and growth of bacterial microbes in variably saturated soils. This numerical model captures three major propagation mechanisms of bacteria in a variably saturated soil as a porous medium, including natural diffusion, bacteria...