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.