A two-dimensional mathematical model was developed to simulate transport phenomena of chemotactic bacteria in a sand-packed column designed with structured physical heterogeneity in the presence of a localized chemical source. In contrast to mathematical models in previous research work, in which bacteria were typically treated as immobile colloids, this model incorporated a convective-like chemotaxis term to represent chemotactic migration. Consistency between experimental observation and model prediction supported the assertions that (1) dispersion-induced microbial transfer between adjacent conductive zones occurred at the interface and had little influence on bacterial transport in the bulk flow of the permeable layers and (2) the enhanced transverse bacterial migration in chemotactic experiments relative to nonchemotactic controls was mainly due to directed migration toward the chemical source zone. On the basis of parameter sensitivity analysis, chemotactic parameters determined in bulk aqueous fluid were adequate to predict the microbial transport in our intermediate-scale porous media system. Additionally, the analysis of adsorption coefficient values supported the observation of a previous study that microbial deposition to the surface of porous media might be decreased under the effect of chemoattractant gradients. By quantitatively describing bacterial transport and distribution in a heterogeneous system, this mathematical model serves to advance our understanding of chemotaxis and motility effects in granular media systems and provides insights for modeling microbial transport in in situ microbial processes.