The aim of this paper was to test how benthic fauna and biogeochemical properties of sediment will vary in response to similar levels of organic enrichment (induced by fish farming) as a function of bottom-habitat type (i.e., mud versus seagrass/coarse sediments), distance from the enrichment source and depth. Our results showed that samples from silty sediments in the vicinity of fish farms have higher TOC and TON values, higher oxygen consumption, higher PO(4) release and lower benthic diversity. In this context muddy sites are more likely to be identified as impacted/critical, than coarse sediment ones.