Estuaries have high rates of primary production and respiration and can be hotspots for carbon dioxide and methane enriched submarine groundwater discharge. Here, we report high resolution pCO₂, CH₄, δ¹³C–CO₂, δ¹³C–CH₄ and radon (²²²Rn, a natural groundwater tracer) observations along North Creek estuary, Australia (S28°48′, E153°34′) during four spatial surveys over a diurnal cycle in January 2013 (summer). There were distinct tidal and diurnal differences in estuarine pCO₂ and CH₄, which lead to tidal differences of 3.6 fold and 5 fold in the estimated CO₂ and CH₄ diffusive water to air fluxes respectively, and up to a 2.4 fold difference in diurnal flux estimates of CH₄. Carbon stable isotopes revealed tidal and diurnal differences in the source δ¹³C value of CO₂ and CH₄, and minor CH₄ oxidation within the estuary. The CO₂ outgassing rates based on the spatial surveys were different than the outgassing derived from three fixed time series stations along the estuary. There was agreement between the methods in the lower and upper estuary where pCO₂ had a relatively low range over the study (~ 600 μatm and 3000 μatm respectively). However, in the mangrove surrounded mid estuary where pCO₂ ranged from ~ 1450 to 11,000 μatm over a tidal cycle, fluxes estimated by the survey method were ~ 30% of the time series estimates. This study highlights the importance of considering tidal and diurnal variability when estimating the flux of CO₂ and CH₄ from estuaries, and discusses how a combination of diurnal (productivity/respiration) and tidal (groundwater/mixing) processes may drive surface water pCO₂ and CH₄ over short-term time scales.