The hyporheic zone, i.e. the groundwater-surface water interface within riverine/riparian ecosystems, plays a key role in water transport, energy flow and biogeochemical cycling at watershed scales. Water and heat exchange are fundamental processes regulating biogeochemical cycles in the hyporheic zones. To improve the understanding of hyporheic flow and heat transport in meandering streams, high-resolution measurements of water level and temperature, combined with a 3-D coupled model of flow and heat transport in the hyporheic zone of a meandering bend, were carried out during a summer flood season. Results show the distinct spatio-temporal variations of hyporheic water and heat exchange. Flooding events (the incoming flood water generated by the upstream rainfall) and local rainstorm events (the storm or rainfall occurring over the local study area) are major drivers for the coupled processes. Incoming flooding from the upper stream increases the hyporheic water and heat exchange in the riverbed and inner bank leading to the longer intra-meander residence times, and warms the riverbed and riverbanks due to the post-rainfall thermal recovery. Local rainstorm event increases hyporheic water and heat exchange flux both laterally and vertically and cools down the riverbed and riverbanks. The water exchange and thermal regimes in the intra-meander seems more driven by the local exchange flows, while the counterparts in the outer bank are dominated by the regional groundwater flow. The temperatures in the inner banks are 1 to 3 °C higher than those in the outer banks, indicating the better hydrological connectivity between river water and groundwater in the intra-meander. The meander apex is a hot spot for hyporheic water and heat exchange. The results highlight the close coupling among river morphology, hyporheic flow, and thermal heterogeneity in a meander system.