Managed aquifer recharge (MAR) represents a promising technique to cope with increasing water stress worldwide. However, it can be challenging to operate MAR systems, especially concerning clogging. Clogging reduces the infiltration capacity and system efficiency of a MAR facility. Processes that cause clogging are difficult to quantify and assess, and their simulations in MAR schemes have so far been limited. The variably saturated water flow model HYDRUS‐2D was therefore modified to include time‐variable hydraulic conductivities to more realistically represent clogging at the infiltration interface of infiltration basins and recharge wells. An exponential function with a time‐variable scaling factor was implemented into HYDRUS to vary the soil hydraulic conductivity over time during simulations. The new approach was tested, in combination with the reservoir boundary condition, by simulating two‐dimensional cross‐sections of two three‐dimensional laboratory experiments representing recharge from infiltration basins and injection wells. With the help of the time‐variable scaling factor, the increasing ponding depth in both experiments due to progressive clogging was reproduced. Hypothetical simulations with various well configurations, soils, and injection rates indicate that clogging influences the infiltration volumes and subsurface infiltration area, which should be considered during the planning of MAR systems. The approach can be used to evaluate the resulting infiltration capacity numerically and to help with the operation and design of MAR facilities. However, further research is required to fully understand and integrate the processes that lead to clogging at MAR facilities into numerical simulations.