a b s t r a c tNitrogen (N) pollution is a global environmental problem that has greatly increased the risks of both the eutrophication of surface waters and contamination of ground waters. The majority of N pollution mainly comes from agricultural fields, in particular during rice growing seasons. In recent years, a gradual shift from the transplanting rice cultivation method to the direct seeding method has occurred, which results in different water and N losses from paddy fields and leads to distinct impacts on water environments. The N transport and transformations in an experimental direct-seeded-rice (DSR) field in the Taihu Lake Basin of east China were observed during two consecutive seasons, and simulated using Hydrus-1D model. The observed crop N uptake, ammonia volatilization (AV), N concentrations in soil, and N leaching were used to calibrate and validate the model parameters. The two most important inputs of N, i.e., fertilization and mineralization, were considered in the simulations with 220 and 145.5 kg ha −1 in 2008 and 220 and 147.8 kg ha −1 in 2009, respectively. Ammonia volatilization and nitrate denitrification were the two dominant pathways of N loss, accounting for about 16.0% and 38.8% of the total N input (TNI), respectively. Both nitrification and denitrification processes mainly occurred in the root zone. N leaching at 60 and 120 cm depths accounted for about 6.8% and 2.7% of TNI, respectively. The crop N uptake was 32.1% and 30.8% of TNI during the 2008 and 2009 seasons, respectively, and ammonium was the predominant form (74% of the total N uptake on average). Simulated N concentrations and fluxes in soil matched well with the corresponding observed data. Hydrus-1D could simulate the N transport and transformations in the DSR field, and could thus be a good tool for designing optimal fertilizer management practices in the future.