Marine cage aquaculture has the potential to severely impact Posidonia oceanica seagrass meadows and its associated fauna. In order to assess the impact of fish farming in a littoral bay of Corsica, France, physico-chemical (mud and organic matter) and biological (density and compactness of P. oceanica beds and associated macrofauna) variables have been examined in two stations putatively impacted to different degrees (St1 and St2) and in two unimpacted stations (Controls: C1 and C2). Principal Component Analysis of meadow structural variables (shoot density and compactness of matte) and abiotic variables (mud and organic matter percentage into sediment) highlighted differences among stations and, particularly, differences between impacted stations and controls. Results from C1 and C2 totally overlapped. St1 was the station which differed the most from controls. Compared with control stations, St1 and St2 were characterized by higher values of organic matter and mud and by lower values of shoot density and matte compactness. Permutational multivariate analysis of variance (PERMANOVA) did not show significant differences between C1 and C2 in the structure of macrofauna assemblages, whereas significant differences between the two impacted sites and between these and the control conditions emerged. Differences in assemblages were well correlated with the measured abiotic variables. The analysis showed that the species most responsible for difference among stations were typical of muddy sediment with high organic matter content. These species had higher mean abundance values at impacted stations than at controls. This study suggests fish farming determines an increase of organic matter and sedimentation, which resolve in changes in structural properties of the seagrass meadows and, consequently, changes in the associated macrofauna assemblages.