Changes in hydraulic properties of soils and aquifers as a result of biogeochemical transformations, such as bacteria growth and mineral phase precipitation/dissolution, may lead to significant modifications of the groundwater flow field. This affects in turn the migration pathways and transport rates of solutes, and consequently their spatial distribution. The aim of this work is to investigate different aspects of the field-scale evolution of porosity and hydraulic conductivity in saturated porous media due to bacteria development in the pore space. As a part of this study, a new module was developed for PHWAT to add the capability of modeling clogging. PHWAT is a general flow and multi-component reactive transport computer code based on SEAWAT and PHREEQC-2. The new model incorporates several constitutive equations to convert porosity changes to hydraulic conductivity, as well as biomass attachment/detachment dependent on pore water velocity. Spatial distributions of simulated porosity and hydraulic conductivity changes were compared both against published laboratory data and previous modeling results. We concluded that the model is able to reproduce the clogging process in a reasonably accurate way. Nevertheless, the choice of the constitutive equations and selection of their parameters is problematic. We observed that a single relationship may not be suitable to capture the observed behavior as the hydraulic conductivity decreases. Further research needs to be devoted to understand the pore-scale processes contributing to permeability changes. Following model validation, a synthetic yet realistic contamination scenario was set up to study how porosity and permeability reductions induced by microbial oxidation of contaminants interact with existing geological heterogeneities. We observed strongly nonlinear behavior, resulting in the development of complex spatial contaminant distributions. The original heterogeneous distribution of hydraulic conductivity is modified by the clogging, with the creation of preferential paths that may enhance contaminant spread.