Groundwater - surface water exchanges along river systems are crucial processes affecting stream ecosystem health, nutrient cycling, and trace metal bioavailability through strong redox gradients over short spatial-scales. The flux and direction of hyporheic exchange is driven by stream channel configuration, in-stream morphological units, sediment calibre and packing, and pressure dynamics. Increases in stream stage and pressure have the potential to significantly alter hyporheic flowpaths between riffle-pool sequences. This study examines the hydraulic gradients and geochemistry along an urban stream, including their resultant change to a large storm event. Networks of piezometers and temperature sensors were installed in three riffle-pool sequences along a 400-m stream reach. Pools were subject to moderate upwelling during baseflow conditions (vertical hydraulic gradients ~0.1); riffles were strongly downwelling (VHG = -0.4). Daily spirals in temperature in hyporheic porewaters during baseflow conditions supported hydraulic gradient measurements, with <2 °C and <0.4 °C variation at 5-and 25-cm depth in pools, respectively, contrasted by >4.5 °C and >1 °C variation at 5- and 25-cm depth in riffles, respectively. A 68.3-mm event that raised stream stage 20 cm resulted in the temperature profiles becoming isothermal with the stream temperature in both riffles and pools, with varying times to return to baseflow temperature trends (between three and nine days post-event). In line with the streamwater flushing of hyporheic porewater due to this event, dissolved oxygen significantly increased at all depths in riffles and pools. Additionally, dissovled manganese and iron concentrations significantly decreased due to the input of oxygen. The return to baseflow conditions in oxygen, manganese, and iron in the hyporheic waters of the pools took at least 9, 14, and 21 days, respectively. This response was influenced by varying stream morphology between the sample sites. The results of this study demonstrate that river groundwater-surface water exchange is highly dependent on stream hydraulics, and large discharge events in urban stream systems have the capacity to significantly reset biogeochemical patterns for extended periods, with concomitant effects on overall stream ecosystem health.