Heterogeneous macroporous geometries (HMGs) comprise unevenly distributed macropores with depth. A large variety of macropore distributions produce fast water flow and chemical transport that deviate from uniform flow. We analyzed the measured pressure head and outflow in column experiments with a uniform matrix (Exp. I), one central macropore (main bypass) (Exp. II), and HMG (Exp. III) and evaluated the performance of the models HYDRUS-1D and SWAP under these conditions. Two replicate soil columns were prepared with a 62-cm silty loam layer above a 5-cm sandy loam layer. Well-defined infiltration and drainage conditions were applied to top and bottom boundaries, respectively. Pressure head and outflow were measured at short time intervals, and calibration was performed by PEST. Experiment I was conducted to calibrate the matrix parameters and Exp. II to calibrate macropore parameters. In Exp. III, four dead-end macropores were created around the main bypass, and the models were run using the previously calibrated parameters, updating only the macropore geometry parameters. The results indicated that HMGs increased total macropore influx, especially in the internal catchment domain. Interaction between the internal catchment, main bypass, and matrix domains was necessary for explaining the change in cumulative outflow and outflow onset observations. The simulations with both models were accurate for HMG regarding pressure head and outflow. The implicit representation of HMGs by HYDRUS-1D improved outcomes for cumulative outflow, whereas the explicit representation by SWAP improved results for lateral mass transfer. The ability to model the effects of HMGs is essential for environmental and agricultural studies.