Catchment headwaters comprise the majority of all stream length globally, however, carbon (C) dynamics in these systems remains poorly understood. We combined continuous measurements of pCO2 and radon ((222)Rn, a natural groundwater tracer) with discrete sampling for particulate organic, dissolved organic and inorganic carbon (POC, DOC, and DIC) to assess the short-term carbon dynamics of a pristine subtropical headwater stream in Australia, over contrasting hydrologic regimes of drought, flash-flooding and recovery. Observations over 23days revealed a shift from carbon losses dominated by CO2 outgassing under conditions of low flow (66.4±0.4% of carbon export) to downstream exports of carbon during the flood (87.8±9.7% of carbon export). DOC was the dominant form of downstream exports throughout the study (DOC:DIC:POC=0.82:0.05:0.13). The broadest diel variability among variables occurred during the drought phase, with diel variability up to 662μatmd(-1) (or 27μM[CO2*]d(-1)), 17μMd(-1) and 268Bqm(-3)d(-1) for pCO2, dissolved oxygen and (222)Rn, respectively. Diel dynamics indicated multiple interrelated drivers of stream water chemistry including groundwater seepage and in-stream metabolism. The catchment exported terrestrial carbon throughout the field campaign, with a mean net stream flux of 4.7±7.8mmolCm(-2)(catchment area)d(-1) which is equivalent to 1.4±2.3% of the estimated local terrestrial net primary production. Our observations highlight the importance of accounting for hydrological extremes when assessing the carbon budgets and ecosystem metabolism of headwater streams, and provide a first estimate of aquatic carbon exports from a pristine Australian subtropical rainforest.