Bioretention, initially designed for treating discontinuous runoff pollution, has a large challenge in trade-off between the hydraulic retention time (HRT) and its treatment capacity. In this study, six enhanced submerged media together with four HRTs were designed for bioretention cells to treat the highly nitrogenous river water in Tai lake basin in Yangtze River delta, China. Results revealed that bioretention with activated carbon has the highest removal of nitrate (NO3−-N) (93–96%) compared with surfactant-modified activated carbon (SMAC), surfactant-modified zeolite (SMZ), zeolite, fly ash and ceramsite. Although the SMAC had the best absorption for NO3−-N and could desorb NO3−-N when its concentration was low in the submerged layer, the desorbed surfactant could inhibit the growth of denitrifying bacteria, which leads to low removal efficiency (49–66%). The dynamic balancing of NO3−-N desorption and denitrifying system restrain in the SMAC device was observed and explained. The best activated carbon-gravel proportion in the submerged layer was 1:1 (l50 mm). Such design could ensure the stable and efficient NO3−-N removal rate (93–94%) under high inflow concentration (28.9 mg/L) and high hydraulic loading (8.2 cm/h).