AbstractCharacterizing the spatiotemporal variability of water fluxes at the stream‐groundwater interface is extremely challenging due to the lack of methods for estimating hyporheic flows at different scales. To address this, we demonstrate the potential of Active‐Distributed Temperature Sensing (DTS) methods for measuring and mapping hyporheic flow in a lowland stream. Experiments were conducted by burying a few hundred meters of heatable Fiber‐Optic cables within streambed sediments in a large meander, where permanent stream‐losing conditions are observed along the stream reach. We propose a new methodology to filter ambient temperature variations along the heated section of the DTS cable and to extend the application of Active‐DTS to losing streams. After data processing, the results show that, along lateral and longitudinal stream profiles, both thermal conductivity and water flux values follow normal distributions with relatively small standard deviations. Hyporheic fluxes vary by one order of magnitude. The absence of correlation between water fluxes within the hyporheic zone and streambed topography variations suggests that the variability is mainly controlled by local streambed heterogeneities. This means that the spatiotemporal variability of fluxes may be used as a marker of the variability of streambed hydraulic conductivities. The relatively low spatial variability (one order of magnitude) in hyporheic flow suggests a small variability of streambed properties. This is an important result for calibrating models assessing hyporheic processes, in which the hydraulic conductivity distribution is generally assumed. Additionally, measurements made over three years yield similar estimates showing the remarkable stability of hyporheic flows through time.