A mathematical model describing microbial transport and growth in a heterogeneous aquifer domain, composed of overlapping subdomains of high-permeability and low-permeability materials, is developed. Each material is conceptually visualized as a continuum which occupies the entire considered spatial aquifer domain. Based on the assumption that advection in the low-permeability domain is negligible, the mathematical model is solved by using a publically available reactive transport code. The importance of modeling microbial transport and growth in such a dual-porosity system is demonstrated through a hypothetical case study.