1. Community structure of interstitial invertebrates was studied in the sediments of two gravel bars in a bypass section of the Rhone River (France), in relation to hydrological patchiness and to major geomorphological characteristics of the sampling areas. Hydrological patchiness was characterized by upwelling or downwelling zones while geomorphological characteristics were concerned mainly with position towards the head or tail of each bar, which presented different environmental conditions. 2. Longitudinal profiles of the two bars, at 0.5 and 1.0 m below the substrate surface, were compared. At each station 10-l samples were taken using mobile standpipes and a Bou-Rouch pump. During low-water conditions, replicate samples were taken in both the head-bar and tail-bar regions to confirm the results. Physicochemical parameters were used to differentiate surface water from ground water (conductivity, alkalinity, silica, nitrates, sulphates and temperature) and to detect hydrological patterns. 3. Two different situations were observed within the gravel bars. In the first one, the upwelling zone was situated in the tail bar and downwelling zone in the head bar. The reverse was observed in gravel bar 2 where the head-bar region formed the upwelling zone and the tail-bar region formed the downwelling zone. 4. In the first situation, the distribution of interstitial assemblages corresponded with the observed hydrological patterns: epigean fauna characterized the downwelling zone and stygofauna characterized the upwelling zone. The interstitial fauna seemed to be strictly linked to the mode of water movement within the sediments. Hydrological patchiness therefore appeared to be an important factor for the structure of interstitial assemblages. 5. In the second case there was no relationship between the hydrological and the biological pattern. Epigean fauna and hypogean fauna were scattered all along the gravel bar. These results suggest that geomorphology is a second important factor governing the composition and structure of interstitial assemblages. A precise structure was obtained when hydrological and geomorphological characteristics were superimposed (case 1). When they were opposed (case 2) all the species responded according to their individual ecological requirements.