Water and sediment samples were collected from a heavily polluted urban river in the Xianlin University Town of Nanjing. We examined the effects of different aeration ways (aerating to sediments, aerating to water) on migration and transformation of nitrogen, using the indoor experimental method. The results showed that: nitrogen release from sediments in the form of NH4(+) -N that will accumulate under anaerobic conditions with increasing temperature; the maximum accumulation of NH4(+) -N in overlying water showed that aerating to water group < aerating to sediment group < control group and the maximum concentrations reached 9.40 mg x L(-1), 11.24 mg x L(-1) and 19.30 mg x L(-1), respectively; nitrogen compounds were generally eliminated from experiment system by a process of ammonia volatilization and a combination of two processes, i. e. nitrification and denitrification under aerating conditions; aerating to sediment was more effective for nitrogen removal than aerating to water, which was removed from overlying water, pore water and sediment; at the experimental endpoint, the concentrations of NH4(+) -N in pore water and sediment were significantly decreased by 64.36% and 58.73% respectively compared with those before aeration in aerating to sediment group and that were decreased by 39.53% and 38.78% respectively in aerating to water group; during nitrogen transformation process in overlying water, start-up of nitrification was slowly under aerating conditions; it took 9 days to realize nitrification under aerating to water conditions and 16 days under sediment aeration conditions; the NO2(-) -N accumulation took place in overlying water under the condition of aeration; the sustain time of NO2(-) -N accumulating was 17 days in aerating to water group and that was 14 days in aerating to sediment group.