A 3D pore network model was developed to simulate the removal of dextran from water. Advanced scanning electron microscopy combined with focused ion beam analysis was used to obtain the sizes of the different pore networks that represent the microscopic structure of a porous membrane. The required input transport parameters for modeling were obtained by performing dynamic experiments on dextran adsorption within the pores of a polysulfone membrane. The simulated flux changes demonstrated a good agreement with the experimental data showing that such a model can be used to study the effects of various parameters during the process. Specifically, the results showed an increase in the applied pressure, decreased membrane thickness, increased pore size, while small sizes of contaminant molecules lead to a rise of the flux passing through the membrane.