Water table management with controlled drainage and subsurface-irrigation (SI) has been identified as a Beneficial Management Practice (BMP) to reduce nitrate leaching in drainage water. It has also been shown to increase crop yields during dry periods of the growing season, by providing water to the crop root zone, via upward flux or capillary rise. However, by retaining nitrates in anoxic conditions within the soil profile, SI could potentially increase greenhouse gas (GHG) fluxes, particularly N2O through denitrification. This process may be further exacerbated by high precipitation and mineral N-fertilizer applications very early in the growing season. In order to investigate the effects of water table management (WTM) with nitrogen fertilization on GHG fluxes from corn (Zea mays) agro-ecosystems, we conducted a research study on a commercial farm in south-western Quebec, Canada. Water table management treatments were: free drainage (FD) and controlled drainage with subsurface-irrigation. GHG samples were taken using field-deployed, vented non-steady state gas chambers to quantify soil CO2, N2O and CH4 fluxes weekly. Our results indicate that fertilizer application timing coinciding with intense (≥24 mm) precipitation events and high temperatures (>25 °C) triggered pulses of N2O fluxes, accounting for up to 60% of cumulative N2O fluxes. Our results also suggest that splitting bulk fertilizer applications may be an effective mitigation strategy, reducing N2O fluxes by 50% in our study. In both seasons, pulse GHG fluxes mostly occurred in the early vegetative stages of the corn, prior to activation of the subsurface-irrigation. Our results suggest that proper timing of WTM mindful of seasonal climatic conditions has the potential to reduce GHG emissions.