In this study the environmental impacts of two fish farms located over deep water (180-190 m) were compared. MC-Farm was located at a site with slightly higher water currents (mean current speed 3-5 cms(-1)) than LC-farm (<2 cms(-1)). Macrofauna composition, bioirrigation and benthic fluxes (CO2 and NH4(+)) were quantified at different stages of the production cycle, revealing very different impact of the two farms. Macrofauna abundance and bioirrigation were stimulated compared to a non-impacted reference site at MC-farm, while macrofauna diversity was only moderately reduced. In contrast, macrofauna communities and related parameters were severely impoverished at LC-Farm. This study suggests that deep-water fish farms should not be sited in low current areas (<2 cms(-1)), since this will hamper waste dispersal and aggravate environmental impacts. On the other hand, fish farming at slightly more dynamic sites can lead to stimulated benthic macrofauna communities and only moderate environmental impacts.