The eutrophication of water in an urban river was treated by combining two submerged aquatic plants Elodea nuttallii and Potamogeton crispus with a biological growth-promoting agent Bio-energizer (BE) on a pilot scale. The results showed that the two submerged plants could remove CODCr effectively and steadily, with a removal rate of 58% and 52.3% respectively. All experimental treatments were effective at removing TN, TP, NH4+-N, NO3+-N, but the treatment in which BE was added at the lower concentration (from 1 to 3 ml/m3) was better than that at the higher concentration (from 5 to 10 ml/m3). Elodea nuttallii produced the best treatment efficiency when 1 ml/m3 BE was added to the experimental water. The rate of removal of TP and TN was 71.0%, and 72.4% within one week while that in the control group was 50% and 51% respectively. The number of bacteria changed during the different stages of the experiment.