Macropores are important hydrologic features that result in preferential flow and transport even under partially saturated flow conditions. The objective of this study was to use numerical simulations to investigate the hydraulic representation of preferential flow in partially saturated macroporous soils. Tension infiltration experiments that exhibited varying degrees of preferential flow, primarily along worm burrows, provided the basis for the numerical simulations. Field measurements of infiltration, soil water content, and dye transport were used to calibrate the model and assess the results. A three-dimensional model was constructed such that the soil matrix contained discrete vertical macropores. The simulations were able to capture the relevant flow and transport characteristics during infiltration. Sensitivity analyses demonstrated the utility of cumulative infiltration and dye transport data for constraining numerical simulations of macroporous systems. Hydraulic conductivity estimates for both matrix and macropores were lower than expected, which may be due to an overly simplified description of macropore flow hydraulics. Simulated macropore discontinuities near the surface reduced the infiltration volume by >50% and the depth of dye transport by >80%. The simulations also showed that increasing macropore density was nearly linearly related to increases in preferential flow, and confirmed field observations that closer macropore spacing led to increased transport depths due to macropore–matrix interaction and conjoined wetting fronts between neighboring macropores. This discrete macropore approach provides a useful method for examining macropore flow and transport, and highlights gaps in our understanding of the unsaturated flow behavior of macropores.