The purpose of this study was to remove cadmium (Cd) and mercury (Hg) from non-point source wastewater by a hybrid bioreactor consisting of two different processes (anaerobic-anoxic-aerobic and photoautotrophic). The results showed that the bioreactor could concurrently culture heterotrophic and autotrophic microorganisms, and removed Cd and Hg from the wastewater successfully. The average removal efficiencies were 79% and 66%, respectively for Cd and Hg. The relationship between Cd removal rate and biofilm mass was observed to be significant (p < 0.05) during different seasons. The Hg removal was mainly due to the bioaccumulation in macrophytes via a photoautotrophic process. Due to the increase of the bacterial diversity under the rejuvenated conditions modulated by the hybrid bioreactor, the growth conditions of the native bacterial habitat were improved. The results demonstrate that the environmentally benign, easily-deployed, sludge free and cost-effective hybrid bioreactor can efficiently remove Cd and Hg from non-point source wastewater. (C) 2011 Elsevier Ltd. All rights reserved.