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 36 hours 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. Firstly, 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 5 hours of increases in stream discharge comprising over 70% pre-event water. Secondly, 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 9 minutes), which was observed immediately after the heavy rainfall period. Thirdly, δ¹⁸O values were used to calculate a time lag of 20 minutes 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.