Two simulated river bioreactors with elastic filler and AquaMats were applied to remediate micro-polluted source water. Under intermittent aeration and gradual increase of aeration intensity, the biofilm reactor with elastic filler was successful start-up within 50 days, and average removal efficiencies of permanganate index, NH4(+) -N were 78.2% and 93.5%, respectively, but the removal efficiencies of the reactor with AquaMats were more than 70% and 80% after two weeks. On the condition of aerobic to anoxic ratio of 3 h: 3 h and aeration intensity of 250 L x h(-1), elastic filler was more efficient for the removal of permanganate index, NH4(+) -N, TN and TP. The pollutant removal of AquaMats was strongly enhanced when the aerobic to anoxic ratio and aeration intensity changed to 2 h :4 h and 120 L x h(-1), which suggested its potential of energy saving. Microscopic observation revealed that the surface of elastic filler was fully surrounded with filamentous bacteria and more inorganic particulate matter after successful start-up of the reactor, and the biofilm attaching to AquaMats was of higher microbial population diversity. The results indicated that elastic filler with homogeneous biofilm had a strong retention capacity for its radial structure, and the AquaMats with microporous structure was more suitable for the enrichment of different functional microorganisms and enhanced the collaborative removal of multiple pollutants.