Biogeochemical processes in subsurface flow constructed wetlands are influenced by flow direction, degree of saturation and influent loading position. This study presents a simulation tool, which aims to predict the performance of the unit and improve the design. The model was developed using the HYDRUS program, calibrated and verified on previously measured bromide (Br−) pulse tracer tests. Three different hydraulic designs (Horizontal (HF), Vertical upward (VF-up), Vertical downward (VF-down) and two different flow rates: Low (L), and High (H)) were investigated. The model simulated well the Br− transport behaviour and the results underline the importance of the hydraulic design. Calibrated model parameters (longitudinal dispersivity, immobile liquid phase, mass transfer coefficient) showed a common trend for all the designs, for increasing flow rates within the investigated range. The VF-down performed best, i.e. had the highest hydraulic retention time.