For understanding the internal transformations of the nitrogen in nitrogenous contaminants like ammonia nitrogen (NH3-N), nitrite nitrogen (NO2-N) and nitrate nitrogen (NO3-N) in natural waters, the remediation effects of the designed reactors on NH3-N, NO2-N and NO3-N were well carried out, respectively. It was not like the NO3-N contaminants which would be rapidly whittled down within any concentrations of this experiment, meanwhile the concentrations of the NH3-N and NO3-N contaminants were respectively reduced by nitrification and denitrification from 5.00 mg/L and 10.00 mg/L in influents under the conditions of dissolved oxygen concentrations of 5.0 ± 0.6 mg/L and the redox potential (ORP) about + 213 ± 37 mV at 20.0 ± 0.5℃ of water temperature to no more than 2.0 mg/L in effluents. Both NH3-N and NO3-N concentrations were under the limited concentrations of the level V of GB 3838 − 2002 with the help of the aerobic granular sludges (AGS) cultured and collected from the interception-reaction galleries (IRG) of the reactors of characteristics of 0.20–2.00 mm in statistical particle diameter (93 ± 4% m/m), ash contents of 7 ± 5% m/m and the degradation capacities of 0.88 ± 0.13 (mg nitrogen)/(mg sludge). Thereafter, it was not decreased as expected to the finial acceptable concentration of the prospective value of 2.00 mg/L with the original concentration of 15.00 mg/L in influents. Thus, the processes of the nitrogenous contaminants could be remediated within the concentrations of the rage of no more than 10.00 mg/L, especially both NH3-N and NO3-N to friendlily purify the natural waters without any other exogenous powers and more energy consumptions to the environment.