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Abstract Emission of CO₂from tropical peatlands is an important component of the global carbon budget. Over days to months, these fluxes are largely controlled by water table depth. However, the diurnal cycle is less well understood, in part, because most measurements have been collected daily at midday. We used an automated chamber system to make hourly measurements of peat surface CO₂emissions from chambers root‐cut to 30 cm. We then used these data to disentangle the relationship between temperature, water table and heterotrophic respiration (R_het). We made two central observations. First, we found strong diurnal cycles in CO₂flux and near‐surface peat temperature (<10 cm depth), both peaking at midday. The magnitude of diurnal oscillations was strongly influenced by shading and water table depth, highlighting the limitations of relying on daytime measurements and/or a single correction factor to remove daytime bias in flux measurements. Second, we found mean daily R_hethad a strong linear relationship to the depth of the water table, and under flooded conditions, R_hetwas small and constant. We used this relationship between R_hetand water table depth to estimate carbon export from both R_hetand dissolved organic carbon over the course of a year based on water table records. R_hetdominates annual carbon export, demonstrating the potential for peatland drainage to increase regional CO₂emissions. Finally, we discuss an apparent incompatibility between hourly and daily average observations of CO₂flux, water table and temperature: water table and daily average flux data suggest that CO₂is produced across the entire unsaturated peat profile, whereas temperature and hourly flux data appear to suggest that CO₂fluxes are controlled by very near surface peat. We explore how temperature‐, moisture‐ and gas transport‐related mechanisms could cause mean CO₂emissions to increase linearly with water table depth and also have a large diurnal cycle.