Located in the south-west region of Spencer Gulf, South Australia, a multi-million dollar aquaculture industry based on the ranching of southern bluefin tuna (Thunnus maccoyii) contributes significantly to the regional economy. The interaction between aquaculture activities and the environment is of significant interest to industry stakeholders, management authorities and the broader science community. No studies, to the best of my knowledge, have investigated the relationships between the hydrodynamics and biogeochemistry of the system and the ability of the benthic ecosystem to deal with the increased loads of organic material from aquaculture activities. This thesis uses a multi-disciplinary approach combined with modern statistical techniques to explore the linkages between hydrodynamics, sediment geochemistry, sedimentary nutrient cycling and the aquaculture industry. Modelling results have identified that swell entering the mouth of Spencer Gulf from directly south causes the greatest swell heights in the central tuna farming zone. Winds from the north-east through to south-east generate the greatest wind-wave heights in the central tuna farming zone. This is directly related to the available fetch. The energy contained in the locally generated wind waves was the same order of magnitude as that of the dissipated oceanic swells. Yet the incoming swell poses the greatest risk to aquaculture activities as the increased wave length causes swell energy to penetrate to the seafloor. The results of this work suggest that the sediment geochemistry is tightly coupled to both the hydrodynamic regime and the buildup of silt originating from aquaculture activities. In the more exposed regions of the tuna farming zone, periodic resuspension events caused by swell propagating into the area from the Southern Ocean, resuspend fine unconsolidated sediments into the lower 10 m of the water column. This material is then advected through the region by the residual (low-frequency) currents until it settles out in areas of lower energy. This process has created two distinct provinces within the region that can either be classified as depositional or erosional. The combined effect of wave action and tidal currents have generated a heterogeneous distribution of biogeochemical properties within the sediments. Denitrification rates were measured in these heterogeneous sediments using a novel technique based on Bayesian statistics to explicitly account for the spatial variability of the sediment biogeochemistry. The denitrification rates were found to be generally low, largely due to the lack of organic matter entering the sediments. However, adjacent to aquaculture activities, the high organic loads stimulate sedimentary denitrification, with rates reaching values of up to three orders of magnitude greater than the control sites. Denitrification efficiencies were high adjacent to the aquaculture activities, with up to 95% of the dissolved inorganic nitrogen produced from the breakdown of organic matter in the sediments being removed. Variability in the denitrification efficiencies was related to the textural characteristics of the sediments, with high efficiencies in finer sediments. It is proposed that this is due to the lower permeability of these sediments restricting the advective exchange of porewater nutrients.