Constructed wetlands (CWs) are engineered water treatment systems designed to remove various types of contaminants. A large number of processes simultaneously contribute to water quality improvement in CWs. During the last decade, there has been a wide interest in the understanding of complex “constructed wetland” systems, including the development of numerical process-based models describing these systems. A number of process-based numerical models for subsurface flow (SSF) CWs have been developed during the last few years; however, most of them are either in an early stage of development or are available only in-house. The HYDRUS wetland module is the only implementation of a CW model that is currently publicly available. Version 2 of the HYDRUS wetland module includes two biokinetic model formulations simulating reactive transport in CWs: CW2D and CWM1. In CW2D, aerobic and anoxic transformation and degradation processes for organic matter, N, and P are considered, whereas in CWM1, aerobic, anoxic, and anaerobic processes for organic matter, N, and S are taken into account. We simulated horizontal flow CWs using both biokinetic models. Compared with the CWM1 implementation in the RETRASO code, the HYDRUS implementation was able to simulate fixed biomass, which is of high importance for obtaining realistic predictions for the treatment efficiency of CWs. We also compared simulation results for horizontal flow CWs obtained using both CW2D and CWM1 modules that showed that CWM1 produces more reasonable results because it also considers anaerobic degradation processes. The influence of wetland plants on the simulation results was also investigated. Simulated biomass profiles in the filter were completely different when considering O2 release from roots, thus indicating the importance of considering plant effects.