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This work presents a numerical model able to simulate the effect of biomass growth on the hydraulic properties of saturated porous media, i.e., bioclogging. A new module for an existing coupled flow and reactive-transport code -- PHWAT -- was implemented. Laboratory experiments were used to validate the model. Good agreement with the experimental data was found. Model behavior was satisfactory in terms of numerical discretization errors and parameter calibration, although-grid independent results were difficult to achieve. The new code was applied to investigate the effect of the initial conditions on clogging development. A set of simulations was conducted considering 1D and 2D flow conditions, for both uniform and heterogeneous initial biomass concentrations. The simulation results demonstrated that the rate and patterns of bioclogging development are sensitive to the initial biomass distribution. Thus, the common assumption of an initially uniform biomass distribution may not be appropriate and may introduce a significant error in the modeling results.