Water regimes strongly impact soil C and N cycling and the associated greenhouse gases (GHGs, i.e., CO2, CH4 and N2O). Therefore, a study was conducted to examine the impacts of flooding-drying of soil along with application of nitrogen (N) fertilizer and nitrification inhibitor dicyandiamide (DCD) on GHGs emissions. This study comprised four experimental treatments, including (i) control (CK), (ii) dicyandiamide, 20 mg kg-1 (DCD), (iii) nitrogen fertilizer, 300 mg kg-1 (N) and (iv) DCD + N. All experimental treatments were kept under flooded condition at the onset of the experiment, and then converted to 60% water filled pore space (WFPS). At flooding stage, N2O emissions were lower as compared to 60% WFPS. The highest cumulative N2O emission was 0.98 mg N2O-N kg- 1 in N treated soil due to high substrates of mineral N contents, but lowest (0.009 mg N2O-N kg- 1) in the DCD treatment. The highest cumulative CH4 emissions (80.54 mg CH4-C kg- 1) were observed in the N treatment, while uptake of CH4 was observed in the DCD treatment. As flooded condition converted to 60% WFPS, CO2 emissions gradually increased in all experimental treatments, but the maximum cumulative CO2 emission was 477.44 mg kg- 1 in the DCD + N treatment. The maximum dissolved organic carbon (DOC) contents were observed in N and DCD + N treatments with the values of 57.12 and 58.92 mg kg- 1, respectively. Microbial biomass carbon (MBC) contents were higher at flooding while lower at transition phase, and increased at the initiation of 60% WFPS stage. However, MBC contents declined at the later stage of 60% WFPS. The maximum MBC contents were 202.12 and 192.41 mg kg- 1 in N and DCD + N treatments, respectively. Results demonstrated that water regimes exerted a dramatic impact on C and N dynamics, subsequently GHGs, which were highly controlled by DCD at both flooding and 60% WFPS conditions.