We investigated the environmental factors that control the local composition and distribution of hyporheic invertebrates within the sediments of a 3rd-order prealpine gravel-bed stream (Töss River, Switzerland). We focused on faunal gradients as functions of environmental conditions reflecting 1) hydrological exchange patterns, 2) sediment depths, 3) physicochemical and fine particle gradients, and 4) interactions between these 3 factors. Three clustered sets of steel piezometers were installed at 4 depths in the sediment (20, 50, 100, 150 cm) at locations with distinctly different types of hydrological exchange (infiltration, exfiltration, horizontal advection) to obtain samples of the fauna and the physicochemical and sedimentological conditions. Sixty taxa were identified, the most abundant of which were cyclopoid copepods (33%), ostracods (23%), and chironomids (11%). Total animal density patterns were strongly related to the ratio of particulate organic carbon to total fine particles (POC/TFP), which explained 61% of the variation in abundance within the sediment. Gradients in hyporheic community structure corresponded most to changes in POC/TFP, hydrological variables, and distance between the surface and groundwater habitats. Interstitial POC/TFP was determined mainly by the interaction between sediment depth and type of hydrological exchange in conjunction with season. The POC/TFP optima for individual taxa indicated that the depth to which epigean taxa penetrate sediments may be restricted by availability of the food resource, which decreases with decreasing POC/TFP. Therefore, the proportion of fine inorganic particles appears to be a critical determinant of the availability of food resources for interstitial invertebrates.