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Abstract Climate change is exposing coastal landscapes to more flooding, in addition to rapidly rising temperatures. These changes are critical in the Arctic where the effects of sea level rise are exacerbated by the loss of sea ice protecting coasts, subsidence as permafrost thaws, and a projected increase in storms. Such changes will likely alter the land-atmosphere gas exchange of high-latitude coastal ecosystems, but the effects of flooding with warming remain unexplored. In this work we use a field experiment to examine the interacting effects of increased tidal flooding and warming on land-atmosphere CO₂and CH₄exchange in the coastal Yukon–Kuskokwim Delta, a large sub-Arctic wetland and tundra complex in western Alaska. We inundated dammed plots to simulate two levels of future flooding: low-intensity flooding represented by one day of flooding per summer-month (June, July and August), and high-intensity flooding represented by three-consecutive days of flooding per summer-month, crossed with a warming treatment of 1.4 °C. We found that both flooding and warming influenced greenhouse gas (GHG) exchange. Low-intensity flooding reduced net CO₂uptake by 20% (0.78µmol m⁻²s⁻¹) regardless of temperature, and marginally increased CH₄emissions 0.83 nmol m⁻²s⁻¹(33%) under ambient temperature, while decreasing CH₄emissions by −1.96 nmol m⁻²s⁻¹(40%) under warming. In contrast, high-intensity flooding restored net CO₂uptake to control levels due to enhanced primary productivity under both temperature treatments. High-intensity flooding decreased CH₄emissions under ambient temperature by 0.76 nmol m⁻²s⁻¹(30%), but greatly increased emissions under warming by 4.68 nmol m⁻²s⁻¹(265%), presumably driven by increased plant-mediated CH₄transport. These findings reveal that GHG exchange responds rapidly and non-linearly to intensifying flooding, and highlight the importance of short-term flooding dynamics and warming in shaping future carbon cycling in this Arctic coastal wetland.