Hydroacoustic data collected during two echosurveys carried out in the Sicily Channel in 1998 and 2002 were analysed to investigate the distribution and spatial structure of small pelagic fish species in relation to the sedimentological nature of the sea bottom. The study was carried out on two contiguous areas (labelled ZONE 1 and ZONE 2) of the continental shelf off the southern coast of Sicily, characterised by different dominant texture, ‘sand’ for ZONE 1 and ‘clayey‐silt’ for ZONE 2. Simultaneous information on small pelagic fish schools and the seabed was obtained using a quantitative echo‐sounder (SIMRAD EK500) that measures echoes due to the scattering from both fish schools and the bottom surface. Acoustically determined fish school and seabed data were integrated, respectively, with information on species composition obtained by experimental fishing hauls, and with granulometric information obtained from the analysis of in situ sediment samples. The results indicate a general preference of small pelagic fish schools for seabeds of finer granulometry. First, the occurrence of fish schools was higher over the acoustically classified ‘soft’ seabeds of ZONE 2. Secondly, although ZONE 2 represents <30% of the total length of daytime acoustic tracks analysed in this study, in both surveys the bulk of fish biomass (>60%) was concentrated over ‘soft’ seabed substrates of ZONE 2. Different species composition and/or behaviour of fish schools in the two areas investigated were postulated in relation to seabed conditions. Specifically, over the hard and soft bottoms of ZONE 2, fish schools were found at lower depths and at shallower bottom depths compared to ZONE 1. Furthermore, over the softer bottoms of ZONE 2, fish schools exhibiting a more ‘pelagic’ behaviour (i.e. detected at a greater distance from the bottom) showed a preference for softer (and finer) seabed substrate conditions. Conversely, fish schools exhibiting a more ‘demersal’ behaviour (i.e. at a smaller distance from the bottom) were mostly found on relatively harder substrates.