The research aimed to improve understanding of the environmental interactions of Atlantic Salmon farming and provide recommendations for monitoring and management strategies. The study focused on three regions in Tasmania: Macquarie Harbour, Storm Bay, and the southern end of the D'Entrecasteaux Channel. A comparison of sediment characteristics revealed differences in faunal abundance, species richness, sediment grain size, and sediment redox levels among the regions. Macquarie Harbour had depauperate sediments with low faunal abundance, fine grain size, and anaerobic conditions, while Storm Bay and the Southern Channel supported diverse and species-rich communities with aerobic sediments. The isotopic signatures of sediments indicated different organic matter sources, with Macquarie Harbour showing greater terrestrial and freshwater inputs. The study also highlighted the potential for nutrient inputs from salmon farming to interact with reef ecosystems, necessitating careful consideration in monitoring programs and data interpretation. The commercially available models DEPOMOD and NewDEPOMOD performed well in predicting sediment deposition, with NewDEPOMOD demonstrating improved accuracy in complex bathymetry and dispersive sites. These findings contribute to the development of sustainable farming practices and appropriate monitoring and management strategies for Atlantic Salmon farming.