The physical factors that have been reported to affect primary and secondary production in the Southern Ocean are examined and critically reviewed. Long time series of physical measurements from the Southern Ocean are available and there is a theoretical base from which models can be constructed. In contrast, there are few large-scale measurements of biological parameters and a paucity of long-term biological data sets for the Antarctic region. The absence of predictive models for the biological systems of the region is underpinned by the absence of theoretical understanding of the variations in the physical environment and their effects on primary, secondary, or tertiary production. To further this understanding, we have examined some of the major seasonal and interannual physical data available for the region (sea ice extent and retreat rate, wind stress, and surface ocean circulation patterns) and have examined their relationship to spatial and temporal variation in satellite-derived proxies of primary productivity (Sea-viewing Wide Field-of-view Sensor (SeaWiFS) ocean color data). The results indicate that there are regional differences in the dominant physical forcings and that simple models will fail to replicate the observed patterns of primary production. We have also used the dynamics of Antarctic krill in the South Atlantic as an example to develop a model and explore the various hypotheses that have been put forward to explain interannual variability in this region. Results from this model indicate that the physical system may change in ways that cause periodic shifts in the relative importance of the factors that affect secondary production. The implications for the design of future research programs are explored.