Eutrophication is a widespread global scale pollution problem. Agricultural areas are generally the main contributors to eutrophication, whereas sewage and industrial discharges, which usually receive some treatment prior to discharge, are a secondary source. This is mostly the case of the ultra-oligotrophic Florida Everglades, where natural water sources are often enriched by nutrients from large-scale industrial agricultural stormwater runoff. Remediation of these agricultural waters cannot be conducted with the usual environmental engineering solutions, and in this context ecological engineering approaches such as constructed wetlands are much more suitable. Moreover, these wetlands provide other ecosystem services such as carbon sequestration or habitat provisioning. In this paper we have implemented a mechanistic phosphorus model into a time-space-dependent mathematical simulation platform (COMSOL Multiphysics™) which has been calibrated with wetland mesocosm data. Subsequently we have evaluated different characteristics of constructed wetland physical elements such as internal walls and baffles, different types of inlets, parallel and series operation, and increase in hydraulic retention time (HRT) to study total phosphorus (TP) removal performance and to improve efficiency. Simulation results indicate that wetland mesocosm soils released dissolved organic phosphorus which was washed out together with the effluent, making very difficult to attain a concentration lower than a target of 10 µg TP L-1, as required to protect the Everglades. Simulations showed that the design based on combination of the bottom inlet together with parallel operation extensively improves efficiency. Target TP concentrations can be achieved with this design together with an increase on 25% of hydraulic retention time. With this study we demonstrate the usefulness of the model for detailed designs, opening the door for its use in field scale applications.