We observed ice formation and water column attributes in four shallow Antarctic ponds between January and 7 April 2008. During that time ponds went from ice-free to > 80 cm thick ice, near-freshwater to hypersaline, well-lit to near darkness and temperatures fell to below zero. Here we examine shifts in biological activity that accompanied these changes. During February, freeze-concentration and ongoing photosynthesis increased dissolved oxygen concentration to up to 100 mg l-1, with a near-equivalent decrease in dissolved inorganic carbon and a pH rise. Benthic photosynthesis was responsible for 99% of estimated biological oxygen production. Net oxygen accumulation ceased in late February, pH began to fall and inorganic carbon to increase, but the pool of dissolved oxygen was depleted only slowly. Anoxia had been attained in only one pond by April and there was little accumulation of indicators of anaerobic activity. The nitrogen and phosphorus balances of the ponds were dominated by organic forms, which, like DOC and CDOM, behaved conservatively. Conversely, inorganic nitrogen and phosphorus uptake was evident throughout the study period, at a molar ratio of 16N:1P in two of three ponds, consistent with uptake into biological material. We found no coupling between N and P uptake and photosynthesis.