Spatial and temporal flow dynamics within the hyporheic zone, particularly hyporheic transport and exchange, are important processes and key to ecosystem health with enhanced degradation of micro-pollutants and stream denitrification. The application of heat is widely used as a tracer to determine flux in the hyporheic zone, however, most applications only consider 1D flow. Hence, this data demonstrates how 3D flow fields in the hyporheic zone can be measured.Time series temperature data from the 56 sensor array of the active heat pulse sensor (HPS) Hot Rod from a sand tank experiment under different flow scenarios as well as data collected from a field site in the Mount Lofty Ranges, South Australia are provided.