A dynamic mathematical model, based on the biochemical kinetic processes dominated in shallow free water systems was developed following the Activated Sludge Model (ASM) methodology. The model predicts plant mass and water uptake rate, BOD5 and total nitrogen (TN) removal on a year round basis, given climatic data (temperature and rain variation). The model was developed based on the operation of two parallel pilot-plant basins, one with plants and one without. The dynamic model was used for the design of full scale constructed wetland facilities for given effluent quality requirements (average annual values of 25 mg l-1 BOD5 and 15 mg l-1 TN). It is demonstrated that given inflow information, climatic data and effluent requirements, the required surface area to achieve adequate treatment while securing treated water effluent throughout the year can be determined. In addition, the required initial planting and the amount of plant mass that needs to be cropped on an annual basis is determined. It is also demonstrated that given a total wetland surface, the system performance is optimized if the wetland is divided into two sequential basins, the first with and the second without plants.