Excess nitrogen in urban river networks leading to eutrophication has become one of the most urgent environmental problems. Combinations of different aeration and biofilm techniques was designed to remove nitrogen from rivers. In laboratory water tank simulation experiments, we assessed the removal efficiency of nitrogen in both the overlying water and sediments by using the combination of the aeration and biofilm techniques, and then analyzed the transformation of nitrogen during the experiments. Aeration (especially sediment aeration) combined with the biofilms techniques was proved efficient in removing nitrogen from polluted rivers. Results indicated that the combination of sediment aeration and biofilms, with the highest nitrogen removal rate from the overlying water and sediments, was the most effective combined process, which especially inhibited the potential release of nitrogen from sediments by reducing the enzyme activity. It was found that the content of dissolved oxygen in water could be restored on the basis of the application of aeration techniques ahead, and the biofilm technique would be effective in purifying water in black-odor rivers.