Sediment biogeochemical processes weremeasured on a transect of 4 stations FF 20W, 40W and 80W (number is metres from the fish farm, FF, to the west) at the Ardag gilthead seabream Sparus aurata farm in the Gulf of Aqaba, a highly oligotrophic system renowned for its clear water and diverse corals. At each station samples were taken for analysis of macrofaunal community and benthic oxygen demand, together with depth profiles of CHN, porosity, chlorophyll a and fatty acids. The macrobenthos was dominated by the small marine snail Nassarius sinusigerus. Incontrast tomanyfish farms in temperatewaters, a large abundance of small, opportunist worms was not observed near the fish farm although sulphide oxidising bacteria Beggiatoa spp. were observed. Oxygen demands (108–154 mmol m−2 d−1) near the farm were lower than those observed elsewhere despite the high water temperature (~26 °C). Bioturbation rates derived from chlorophyll profiles were low (0.013– 0.069 cm2 d−1) compared to results froma farmin Scotland as a consequence of themuch lower infaunal abundance. Porosity, organic carbon and carbon/nitrogen ratio profiles showed clear discrimination between the stations near the cages (FF and 20W) and thosemore distant. A Multi-Dimensional Scaling plot of 31 sediment fatty acid concentrations from each of the 4 stations (averaged to 4 cm sediment depth) shows a trend in fatty acid composition that allows good discrimination between 80W, 40W and the two stations near the farm, which overlap. An increase in the proportion of bacterial fatty acids with distance from the farm indicates a change from profiles dominated by farm wastes (with a high proportion of fish feed derived mono-unsaturated fatty acids) near the farm to background conditions where the profiles are dominated by benthic biomass. The data presented are discussed by contrasting these with earlier studies in mesotrophic systems. The results indicate that the Pearson–Rosenberg paradigmof benthic succession may be altered owing to the dominance of the benthos by N. sinusigerus and low animal abundance and so benthic indicators of impact would have to be tailored for the characteristics of this environment. Sediment water content, organic carbon content, C/N ratios and fatty acids all showed trends with distance fromthe farmand could be considered as indicators, as could the density of N. sinusigerus and the presence of Beggiatoa sp. mats.