The impact of repeated hydropeaking events was assessed in the Alpine stream Noce Bianco (Trentino, NE Italy). Three stations were selected, one upstream and two at 0.25 km and 6 km downstream from a hydropower plant which causes 7-fold discharge increases. We collected hyporheic invertebrates for two years. Taxa diversity and abundance were reduced in the impacted sites, especially affecting the stygobites, which were significantly less abundant at the impacted sites, whereas stygoxene invertebrates increased exponentially. Repeated hydropeaking events alter the physical-chemical characteristics of the hyporheic habitat, resulting in the recorded faunistic pattern. The deposition of the fine sediment transported by the turbinated water downstream of the power plant and the absence of natural peak floods which remove fine sediments, probably cause a reduction of the interstitial space interstitial habitat available to stygobitic taxa. Surface water natural thermal regime is altered by the hypolimnetic discharges, and such alterations propagate into the hyporheic, affecting the stenothermic taxa. Some benthic taxa used the hyporheic habitat as a refuge to avoid catastrophic drift during hydropower production operation. The main trophic roles represented in the hyporheic assemblages do not support an important role for biological interactions such as predation in determining the fine-scale patchiness of the hyporheos.