A large pilot-scale free water surface (FWS) constructed wetland polishing effluent from an annual (spring) discharge municipal lagoon was operated for ten years followed by eleven years of dormancy and then restarted with an increase in operating depth. No significant effect of system aging was observed on Biological Oxygen Demand (BOD), total phosphorus (TP), and soluble reactive phosphorus (SRP) removal efficiencies, although internal TP water column concentrations in the first wetland and pond cells increased with time due to resuspension of accumulated sediments. Nitrate and ammonium removal efficiencies were higher during the start-up period due to plant establishment, while organic nitrogen and nitrate removal efficiencies increased during the restart period, likely due to a combination of the increased operating depth and accumulated sediments. No seasonal temperature effect was observed for nitrate or BOD removal efficiency, however, TP removal efficiencies increased with increasing influent concentrations due to seasonal algae growth. TSS removal efficiency increased significantly during the restart period, most likely due to an increase in the operating depth. Phosphorus was found to be mostly stored in the soil, followed by sediment and plants, while nitrogen was found to be stored more in plants, followed by soil and sediment. The wetland system was shown to be effective at the long-term removal of organic matter (BOD5 < 10 mg/L) and TP (87% average removal efficiency), while TSS removal efficiency increased to 97% with an increase in operating depth from 25 to 50 cm.