The overall impact that plant invasions have on greenhouse gas emissions (GHG) by plant-mediated effects and how these interact with environmental and management factors is largely unknown. To address this, we report on the effects of leaf removal and waterlogging, either singularly or in combination, on the fluxes of CO2 and N2O associated with the invasive species Gunnera tinctoria. Both the removal of leaves with and without flooding resulted in higher CO2 emissions due to reductions in photosynthesis. Whilst waterlogging alone was also associated with a reduction in photosynthesis, this was slower than the effect of leaf removal. Significant N2O emissions were associated with intact plants, which increased immediately after leaf removal, or seven days after waterlogging with or without leaf removal. We found positive correlations between CO2 and N2O emissions and petiole and rhizome areas, indicating a size-dependent effect. Our results demonstrate that intact plants of G. tinctoria are a source of N2O emissions, which is enhanced, albeit transiently, by the removal of leaves. Consequently, management interventions on invasive plant populations that involve the removal of above-ground material, or waterlogging, would not only reduce CO2 uptake, but would further compromise the ecosystem GHG balance through enhanced N2O emissions.