Spencer Gulf has extensive seagrass, and is a focus of aquaculture, which accounts for 95% of anthropogenic nutrients. There have been persistent concerns around the impacts of these nutrients on seagrass health and extent, with broadscale monitoring showing declines across much of the gulf. Repeated video sampling at each of three sites inside and outside the predicted nutrient plume from aquaculture in both northern and southern Spencer Gulf showed no changes in seagrasses due to aquaculture. Similar EPA data showed broadscale decline at many sites, probably due to the cumulative effects of a range of stressors. In situ sampling of seagrass morphology and biomass also failed to show any impacts from aquaculture. All sites, however, showed an overall decline in biomass, indicating that the broadscale decline is ongoing. A model of seagrass growth broadly predicts their distribution, although currently underpredicts shoot densities and epiphyte loads. The model indicates areas where aquaculture may cause a decline in seagrass, and others where it may enhance growth. Declines in the model are due to increased turbidity and epiphytes leading to decreased light in deeper waters, while increases are due to a release from nutrient limitation in shallower waters where light is not limiting.