Spatial and temporal effects of fish farming on the benthic community structure at 2 fish farms in the Eastern Mediterranean were investigated between July 2004 and April 2005. In the area of each fish farm, 3 stations were sampled. At each station, sediment samples were collected for analysis of organic carbon, organic matter and benthic community parameters. There were statistically significant differences in organic matter and organic carbon among all stations. This impact seems to be only spatial, since 1-way ANOVA indicated no significant differences in organic matter and organic carbon between seasons for both farms. Furthermore, significant differences were found in species number, abundance and species richness among stations and seasons for one of the farms (2-way ANOVA). One-way ANOVA indicated that the significant differences, detected in the benthic community parameters of this farm, were spatio-temporal for species number, temporal for abundance and spatial for species richness. The spatial effect of fish farming on benthic community structure was present up to 50 m from the centre of cages on one farm and between 50 and 300 m from the other farm. Capitella capitata was the most dominant species at the farm sites, while Nephthys hystricis was the most dominant species at the control sites. In all cases, the benthic assemblages in the immediate vicinity showed symptoms of disturbance, but the spatial and temporal extent of this effect was less than one would expect considering the fact that the study area is located in a semi-enclosed gulf.