Vertical temperature profiles using the 1D analytical solution are now widely used to determine hyporheic flow patterns and hydraulic dynamics within the shallow streambed sediment. One of the challenges in using a limited number of measurements to characterize processes that are essentially 3D has been the determination of the horizontal or lateral flow components and how these vary in magnitude, as well as spatially. This study used a portable 56 sensor, 3D temperature array with 3 heat pulse sources (the hot rod) to measure the flow direction and magnitude up to 230 mm below the water-sediment interface in sedimentary environments ranging from fine silt to coarse gravels. Short heat pulses, typically 1 minute in duration were injected at one of the three heat sources and the temperature response was monitored over a period of 20-30 minutes. Breakthrough curves from each of the temperature sensors was analysed using a heat transport equation and an optimization function was used to estimate flux in three directions to determine the dominant direction and magnitude at the point of observation. Measurements were also conducted in a sand tank under a range of controlled hydraulic conditions to validate the method and to compare the results with a numerical model. The robust design of the hot rod and use of short duration heat pulses provides a rapid, accurate assessment technique for determining dynamic and multi-directional flow patterns in the hyporehiec zone and understanding biogeochemical processes at the water-streambed interface.