Retention of surface-modified nanoscale zero-valent iron (NZVI) particles in the porous media near the point of injection has been reported in the recent studies. Retention of excess particles in porous media can alter the media properties. The main objectives of this study are, therefore, to evaluate the effect of particle retention on the porous media properties and its implication on further NZVI particle transport under different flow conditions. To achieve the objectives, a one-dimensional transport model is developed by considering particle deposition, detachment, and straining mechanisms along with the effect of changes in porosity resulting from retention of NZVI particles. Two different flow conditions are considered for simulations. The first is a constant Darcy’s flow rate condition, which assumes a change in porosity, causes a change in pore water velocity and the second, is a constant head condition, which assumes the change in porosity, influence the permeability and hydraulic conductivity (thus Darcy’s flow rate). Overall a rapid decrease in porosity was observed as a result of high particle retention near the injection points resulting in a spatial distribution of deposition rate coefficient. In the case of constant head condition, the spatial distribution of Darcy’s velocities is predicted due to variation in porosity and hydraulic conductivity. The simulation results are compared with the data reported from the field studies; which suggests straining is likely to happen in the real field condition.