In this paper, we develop a network model to determine porosity and permeability changes in a porous medium as a result of changes in the amount of biomass. The biomass is in the form of biofilms. Biofilms form when certain types of bacteria reproduce, bond to surfaces, and produce extracellular polymer (EPS) filaments that link together the bacteria. The pore spaces are modeled as a system of interconnected pipes in two and three dimensions. The radii of the pipes are given by a lognormal probability distribution. Volumetric flow rates through each of the pipes, and through the medium, are determined by solving a linear system of equations, with a symmetric and positive definite matrix. Transport through the medium is modeled by upwind, explicit finite difference approximations in the individual pipes. Methods for handling the boundary conditions between pipes and for visualizing the results of numerical simulations are developed. Increases in biomass, as a result of transport and reaction, decrease the pipe radii, which decreases the permeability of the medium. Relationships between biomass accumulation and permeability and porosity reduction are presented.