Sediment-dwelling zoobenthos stimulate the mineralization of organic matter and alter nutrient cycling by aerating the sediment via burrows, by feeding on detritus, and by redistributing particles. Here we experimentally revealed that abundant benthic chironomids (Chironomus riparius) can perceive predatory fish (Rutilus rutilus) via chemical cues (kairomones) and spend less time foraging at the sediment surface and more time hiding in their burrows. This predator avoidance behavior significantly increased the exposure of freshly deposited organic particles to oxygen by reducing their burial to subsurface layers and by enhancing the aeration of subsurface layers via burrow ventilation, conditions that together increased the rate of organic matter mineralization. These results demonstrate that predatory fish can exert trait-mediated effects on benthic communities that in turn alter basic ecosystem processes related to nutrient cycling.