Abstract Nitrate-nitrogen (NO−3-N) dynamics and nitrogen (N) budgets in rice (Oryza sativa L.)-wheat (Triticum aestivum L.) rotations in the Taihu Lake region of China were studied to compare the effects of N fertilizer management over a two-year period. The experiment included four N rates for rice and wheat, respectively: N1 (125 and 94 kg N ha−1), N2 (225 and 169 kg N ha−1), N3 (325 and 244 kg N ha−1), and N0 (0 kg N ha−1). The results showed that an overlying water layer during the rice growing seasons contributed to moderate concentrations of NO−3-N in sampled waters and the concentrations of NO−3-N only showed a rising trend during the field drying stage. The NO−3 -N concentrations in leachates during the wheat seasons were much higher than those during the rice seasons, particularly in the wheat seedling stage. In the wheat seedling stage, the NO−3-N concentrations of leachates were significantly higher in N treatments than in N0 treatment and increased with increasing N rates. As the NO−3-N content (below 2 mg N L−1) at a depth of 80 cm during the rice-wheat rotations did not respond to the applied N rates, the high levels of NO−3-N in the groundwater of paddy fields might not be directly related to NO−3-N leaching. Crop growth trends were closely related to variations of NO−3-N in leachates. A reduction in N application rate, especially in the earlier stages of crop growth, and synchronization of the peak of N uptake by the crop with N fertilizer application are key measures to reduce N loss. Above-ground biomass for rice and wheat increased significantly with increasing N rate, but there was no significant difference between N2 and N3. Increasing N rates to the levels greater than N2 not only decreased N use efficiency, but also significantly increased N loss. After two cycles of rice-wheat rotations, the apparent N losses of N1, N2 and N3 amounted to 234, 366 and 579 kg N ha−1, respectively. With an increase of N rate from N0 to N3, the percentage of N uptake in total N inputs decreased from 63.9% to 46.9%. The apparent N losses during the rice seasons were higher than those during the wheat seasons and were related to precipitation; therefore, the application of fertilizer should take into account climate conditions and avoid application before heavy rainfall.