Constructed wetlands serve as both a pollutant sink as well as a possible greenhouse gas source for runoff treatment. Since environmental parameters controlling these biogeochemical cycles can be controlled, it is important to understand how changes in these parameters can affect nutrient and greenhouse gas cycling and concentrations. Thus, we chose to examine the effects of two poorly-understood parameters, the presence of aerenchymal roots and flow rate, by measuring concentrations of several nutrients and gases on two heavily controlled mesocosm constructed wetlands planted with Schoenoplectus acutus and maintained at either high flow (20 ml/min) or low flow (10 ml/min). There was no difference in overall nitrate removal efficiency between the two mesocosms. However, our results indicate that increased flow rate was associated with higher oxygen and nitrate concentrations in the porewaters. The presence of aerenchymal roots increased methane and decreased nitrous oxide concentrations as compared with substrate containing no roots. The differences in methane and nitrous oxide patterns may be due to aerenchymal plants competing for N-uptake with microbes and highlights the importance of species diversity and richness in studying the impact of plants on wetland control. The study also demonstrated the key role that subsurface flow rates, and the associated property of hydraulic retention times, can play in the biogeochemical functioning of constructed wetlands.