Reed stands may be employed in the amelioration of water quality or even in the treatment of wastewater. In this study, the nutrient concentrations of (i) the above- and below-ground Common Reed (Phragmites australis) biomass, and (ii) surface and interstitial water were analyzed in a natural stand used in wastewater treatment. The reed stand was located in Hungarian part of Lake Fertő/Neusiedler See, by the shore near Fertőrákos Bay. The nitrate, phosphate and dissolved organic nitrogen concentrations of surface water were found to be higher on the inlet side of the reed stand compared to the outlet. The N and P concentrations in the above-ground biomass and P concentrations in the below-ground biomass increased after the introduction of pre-treated wastewater. The inter-annual differences in the characteristics of sediment interstitial water and in the nutrient content of reed tissues were assessed using statistical methods. The samples taken before and after the introduction of the pre-treated wastewater in the parcel formed different clusters. The results of the study provide further evidence that the nutrient retention capacity of natural stands of P. australis may be employed in the treatment of wastewater while protecting and preserving the valuable natural assets of the lake.