Estuaries experience tidal and daily variability in both atmospheric and seawater temperatures. This makes shallow estuary ecosystems vulnerable to the effects of climate change, particularly heat stress. Little is known about the role of intertidal soft sediment ecosystems in the carbon cycle and the influence of heat stress. We conducted a multi-day heat stress experiment at two intertidal sites (sandy/muddy) in Waihi estuary, Bay of Plenty, New Zealand, to test the responses of biodiversity and ecosystem functions (methane (CH4) and carbon dioxide (CO2) fluxes). At each site, mini glasshouses were deployed for 4 hours during daytime low tides for 5 or 7 consecutive days (short and long duration heat stress treatments, respectively). CO2 and CH4 fluxes were measured from treatment and control plots on days 2, 5 and 7, and sediment cores were collected to characterise the benthic community and sediments at the end of the experiment. Results showed higher CH4 effluxes where sediment mud content is higher, and increases in CH4 flux following heat stress. Sediments showed uptake of CO2 that reduced following heat stress. Our study has implications for the management of estuaries; increasing muddiness coupled with rising temperatures may change the carbon source/sink status of these ecosystems.