Vertical profiles of temperature, radon and electrical conductivity are used to characterise downwelling, neutral and upwelling hyporheic zones along a pool-riffle sequence in the Haughton River in north-eastern Australia. Water residence times and vertical fluxes are derived from temperature and radon data and then directly compared for downwelling profiles. Temperature and radon-derived fluxes in downwelling zones ranged from 0.02 to 24mday-1 with a mean of 1.69mday-1 while residence times across the study site ranged from tens of minutes to greater than 15days. The radon approach has the lowest uncertainty for residence times between 0.1 and 15days while the uncertainty of the temperature approach (using a diel river signal) is lowest for residence times that are less than a few days. For 83% of depths in downwelling profiles, radon-derived residence times were greater (some up to two orders of magnitude greater) than temperature-derived residence times. When the error bounds of the residence time estimates were accounted for, 57% of radon-derived residence times were considerably greater than temperature-derived residence times in downwelling profiles. We suggest that this disparity is due to the different influence of small scale heterogeneity on temperature and radon transport. These field based results indicate that small scale heterogeneity may play a far more important role than has been previously considered in groundwater-surface water interaction studies.