This research evaluates the effect of both organic and ammonia loading rates and the presence of plants on the removal of chemical oxygen demand and ammonia nitrogen in horizontal subsurface flow constructed wetlands, 2 years after the start-up. Two sets of experiments were carried out in two mesocosms at different organic and ammonia loading rates (the loads were doubled); one without plants (control bed), the other colonized with Phragmites australis. Regardless of the organic loading rate, the organic mass removal rate was improved in the presence of plants (93.4 % higher for the lower loading rate, and 56 % higher for the higher loading rate). Similar results were observed for the ammonia mass removal rate (117 % higher for the lower loading rate, and 61.3 % higher for the higher loading rate). A significant linear relationship was observed between the organic loading rate and the respective removal rates in both beds for loads between 10 and 13 g m−2 day−1. The presence of plants markedly increase removal of organic matter and ammonia, as a result of the role of roots and rhizomes in providing oxygen for aerobic removal pathways, a higher surface area for the adhesion and development of biofilm and nitrogen uptake by roots.