Interannual variability is a characteristic feature of the Southern Ocean ecosystem yet the relative roles of biological and physical processes in generating these fluctuations are unknown. There is now extensive evidence that there are years when there is a very low abundance of Antarctic krill (Euphausia superba) in the South Georgia area, and that the variation affects much of the ecosystem with the most obvious impacts on survival and breeding success of some of the major krill predators. The open nature of the South Georgia ecosystem means this variability has large scale relevance. Fluctuations in year class success in parts, or all, of the population across the Scotia Sea, can generate large changes in the available biomass. The ocean transport pathways maintain the large scale ecosystem structure by moving krill over large distances to areas where they are available to predator colonies. This large scale physical system shows strong spatial and temporal coherence in the patterns of the interannual and sub-decadal variability. This physical variability affects both the population dynamics of krill and the transport pathways emphasizing that both the causes and the consequences of events at South Georgia are part of much larger scale processes.