Abstract The aim of this work was to evaluate the utilization potential of a newly isolated indigenous aerobic denitrifier, Pseudomonas stutzeri strain T1, for nitrogen removal from the eutrophic Lake Taihu in China. The strain was capable of conducting heterotrophic nitrification–aerobic denitrification and had both excellent nitrate and ammonium removal without nitrite build-up. The characteristics of P. stutzeri strain T1 were studied under different cultural conditions. Furthermore, under the optimized cultivation conditions, strain T1 was added into the water samples from Lake Taihu, the ammonium and nitrate removal rates of the strain reached to 60% and 75%, respectively. Via adding this strain, the water qualities of the sample ameliorated from Grade V to Grade II. Thus, the strain T1 should be an useful biological tool to remediate eutrophic lakes and do not meet acclimation problems.