Several climate change scenarios have predicted that heavy precipitation could result in prolonged flooding (PF) and flooding–drying (FD) of soils under agriculture. The influence of PF and FD on soil greenhouse gas (GHG) fluxes and ammonium‑nitrogen (NH4+-N) and nitrate‑nitrogen (NO3−-N) dynamics of arable and grassland soils, the dominant land-use types in the UK, remain unclear. A two-month soil incubation experiment was conducted to determine the impact of PF and FD on soil N dynamics and GHG fluxes from arable and grassland soils. Arable soil emitted more N2O-N when soil moisture exceeded 100% water-holding capacity (WHC) compared to grassland soil under PF. Grassland soils exhibited increased N2O-N emissions than arable soils when soil moisture was lower than 100% WHC under FD. When soil moisture exceeded 100% WHC, the available NO3−-N in the soil contributed 58% of N2O-N emissions potentially by denitrification from grassland. When soil moisture was lower than 100% WHC, soil NH4+-N and NO3−-N contributed 71% of N2O-N emissions, which suggests coupling of nitrification-denitrification processes in driving high emissions from grassland soils. The N2O-N and CO2-C emissions increased with the incubation time under FD. Moreover, FD significantly increased N2O-N, CO2-C, and CH4-C emissions in grassland soil by 0.93, 2.15, and 37.29 times more than arable soil, respectively. These findings points to important tipping points in the source strengths of GHG fluxes from the two land use types differently. Future land use changes should consider the contribution of the changing dynamics of GHG fluxes in light of climate extremes and its implications for net zero greenhouse gas emission ambitions.