A portable Wavelength Scanned-Cavity Ring-Down Spectrometer (Picarro L2120) fitted with a diffusion sampler (DS-CRDS) was used for the first time to continuously measure δ18O and δ2H of stream water. The experiment took place during a storm event in a wet tropical agricultural catchment in north-eastern Australia. At a temporal resolution of one minute, the DS-CRDS measured 2160 δ18O and δ2H values continuously over a period of 36h with a precision of ±0.08 and 0.5‰ for δ18O and δ2H, respectively. Four main advantages in using high temporal resolution stream δ18O and δ2H data during a storm event are highlighted from this study. First, they enabled us to separate components of the hydrograph, which was not possible using high temporal resolution electrical conductivity data that represented changes in solute transfers during the storm event rather than physical hydrological processes. The results from the hydrograph separation confirm fast groundwater contribution to the stream, with the first 5h of increases in stream discharge comprising over 70% pre-event water. Second, the high temporal resolution stream δ18O and δ2H data allowed us to detect a short-lived reversal in stream isotopic values (δ18O increase by 0.4‰ over 9min), which was observed immediately after the heavy rainfall period. Third, δ18O values were used to calculate a time lag of 20min between the physical and chemical stream responses during the storm event. Finally, the hydrograph separation highlights the role of event waters in the runoff transfers of herbicides and nutrients from this heavily cultivated catchment to the Great Barrier Reef.