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Coastal and transitional water ecosystems are amongst the most productive and valuable ecosystems on Earth. For their ecological characteristics they have been largely used for fish farming. The lagoons, in particular, are also important as nursery habitats for fishes and for their role in supporting the economically valuable fishes stocks. Fish farming affects the environmental quality with risks of eutrophication, which can lead to the destruction of the same stock bred and to severe anoxic conditions. Such changes in the physical and chemical characteristics in the sediment can have a strong impact on the structure of the benthic macroinvertebrate communities. Therefore, this work deals with the evaluation of the impact of cage rearing of Sparus aurata, farmed at low and high density, in a Mediterranean coastal lagoon located in Apulia (South Italian coastline). Here the changes in macroinvertebrates community structure and in most common ecological indicators were analyzed. Sediment samples were collected with a box-corer between November 2014 and February 2015 at five stations of the lagoon: two located nearly the cage rearing (high density and low density of S. aurata) while three control sites were located at increasing distance from the rearing cages in areas not impacted by fish farming. In parallel, 75 leaf-bags were submerged in the same five stations (15 leaf-bags per site) and retrieved after 5, 15, 30, 60 and 90 days of exposure. At each sampling occasion, some physical-chemical parameters (temperature, conductivity, pH, dissolved O2, salinity, TDS) were also recorded. Macroinvertebrates collected from box-corer and leaf-bags were identified at lowest possible level and following ecological indicators AMBI, M-AMBI, BENTIX and BITS were calculated. The most evident changes of cage rearing were a significant effect on benthic macroinvertebrate community and an accumulation of nutrients in the sediments of the stations directly interested by fish farming.