Turbulence and aeration are reduced in many streams during low-flow periods as a consequence of drought or water abstraction, thus affecting invertebrate interactions and pivotal ecosystem processes such as the breakdown of organic matter (OM). These effects can be larger in the hyporheic zone (HZ), the ecotone connecting the surface stream and groundwater, especially when fine sediments reduce hydraulic conductivity. In addition, OM breakdown in the HZ could depend on the availability of OM in the benthic zone (BZ), because the latter would not only be a more accessible, and thus preferred, food resource, but also more easily scoured downstream. In a laboratory microcosm experiment of 28 days duration, we manipulated aeration, sediment size and location of OM (either all buried or half buried with half on the surface, simulating the HZ and BZ respectively). Six mayfly (Habroleptoides) individuals and four stonefly (Capnioneura) individuals were enclosed in each microcosm and the consumption of OM was measured. Lack of aeration reduced oxygen saturation from 94 to 66%, reducing OM consumption particularly on the surface, in contrast with our expectations. As hypothesised, the availability of surface OM significantly reduced invertebrate consumption of buried OM. Habroleptoides performed better than Capnioneura, especially in fine sediments. The results suggest that reduced turbulence can affect invertebrate trophic interactions as well as the decomposition of OM, depending on sediment grain size and the location of OM.