This study used a portable 56-sensor, 3-D temperature array with three heat pulse sources to measure the flow direction and magnitude below the water–sediment interface. Breakthrough curves from each of the sensors were analyzed using a heat transport equation. 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.