In order to implement spatial fisheries management in the Arabian Gulf, a better understanding of the distribution of fish in relation to benthic habitats is required. To facilitate this, hydroacoustic fish surveys were conducted over oyster bed/reef (“shallow”) and surrounding soft sediment (“deep”) habitats in the offshore central Gulf, within Qatari waters. Transects at ‘shallow’ sites had significantly higher mean fish density and biomass. Mean target strength of individual fish was also significantly higher at ‘shallow’ sites. Fish positions in the water column were examined and overall there was a closer association with the seabed at the ‘shallow’ sites. Larger fish were found significantly closer to the seabed than smaller fish across all sites, but more so at ‘shallow’ sites than at ‘deep’ sites. Acoustic return from the seabed was extracted to provide information on the habitat type both using ‘Sonar5′ and ‘Visual Habitat’ software. The different site categories (‘shallow’ vs ‘deep’) were significantly different for all the measures of acoustic habitat. Fish density was significantly related to ‘Visual Habitat’ data, more so than depth alone. Our results show that fish distribution in the offshore Gulf is associated with complex, shallow oyster bed/reef habitats, and this is particularly the case for larger demersal fish that are commercially exploited. The ability to characterise benthic habitats from acoustic fish survey data shows promise, with important time saving implications for the monitoring of marine environments and developing a spatial approach to fisheries management. This may include the identification of habitats with a relatively high density of larger fish for inclusion in candidate marine protected areas.