This study examines the use of a numerical model to predict the reduction in permeability of bioclogged specimens observed from column experiments. The numerical model uses the two-dimensional (2D) segmented scanning electron microscope (SEM) images of the initial microstructure of soil and simulates the growth of biofilm assuming uniform grain coating around particles. The corresponding Navier-Stokes equation in free pore space and the flow within the biofilm described by the Brinkman equations are solved using finite-element analysis. The numerical results are shown to match the experimental data very well. The predictions by the different analytical models used in the current literature are also compared. The numerical model, utilizing the uniform grain coating criterion for biofilm growth, is shown to predict well the permeability reduction of porous medium as a function of biofilm saturation.