In this study, the simulation results of four vertical flow wetland systems using the HYDRUS Wetland Module are presented. The four wetland systems comprise three single-stage pilot scale systems and one full-scale two-stage system. The main difference between these systems is the filter media used, referred to as fine media, i.e., sand with a grain size distribution 0.063–4 mm, or coarse media, i.e., sand with grain size distributions between 1–4 mm, respectively. The water-flow simulation of each system is carried out using the single porosity van Genuchten-Mualem model. A good match between measured and simulated volumetric effluent flow rates could be achieved for all wetland systems. For reactive transport simulations, the CW2D biokinetic model was applied. First, simulations were run using the standard CW2D parameter set. For some systems, adjustments of the parameter set were needed in order to avoid unlimited bacteria growth. To better fit measured COD, NH4-N, and NO3-N effluent concentrations, adjustments of few parameters of the standard parameter set were required. The results show that for the VF wetlands with fine sand, no adjustments of the CW2D standard parameter set were needed, while for systems with coarser filter media as the main layer, the standard parameter set had to be adjusted to match simulated and measured effluent concentrations.