Profiles of temperature time series are commonly used to determine hyporheic flow patterns and hydraulic dynamics in the streambed sediments. Although hyporheic flows are 3-D, past research has focused on determining the magnitude of the vertical flow component and how this varies spatially. This study used a portable 56-sensor, 3-D temperature array with three heat pulse sources to measure the flow direction and magnitude up to 200 mm below the water-sediment interface. Short, 1 min heat pulses were injected at one of the three heat sources and the temperature response was monitored over a period of 30 min. Breakthrough curves from each of the sensors were analysed using a heat transport equation. Parameter estimation and uncertainty analysis was undertaken using the differential evolution adaptive metropolis (DREAM) algorithm, an adaption of the Markov chain Monte Carlo method, to estimate the flux and its orientation. Measurements were conducted in the field and in a sand tank under an extensive range of controlled hydraulic conditions to validate the method. The use of short-duration heat pulses provided a rapid, accurate assessment technique for determining dynamic and multi-directional flow patterns in the hyporheic zone and is a basis for improved understanding of biogeochemical processes at the water-streambed interface.