<p>Intertidal estuarine habitats are inundated by seawater and uncovered with every tidal cycle, with potential exposure to both marine and atmospheric heatwaves. Little is known about the role of intertidal soft sediment ecosystems in the carbon cycle and how increasing extreme temperature events may affect carbon flux dynamics. Here we conducted a multi-day experiment simulating a low tide atmospheric heatwave at two estuary intertidal flats (sandy/muddy) to test the responses of macrobenthic biodiversity and fluxes of methane (CH₄) and carbon dioxide (CO₂). Results show heatwave simulation increases CO₂ uptake at the sandy site and causes a switch from efflux (source) to influx (sink) of CO₂ at the muddy site. Raw CH₄ fluxes are unchanged by the temperature treatment but effect sizes relative to controls are greatest in muddy sediments. We provide evidence for cumulative effects of heatwave duration on macrobenthic biodiversity and greenhouse gas fluxes and show that increasing muddiness (often associated with degradation) and increasing duration of heatwave events may change the carbon source/sink status of estuaries.</p>