Energy transfer in microbial food webs is partly quantified by the relationship between bacterial and algal biomass. Tight spatial relationships suggest active bacterial assimilation of dissolved photosynthate in temperate marine and fresh waters. However, studies in the Antarctic suggest that bacterial biomass generation from algal-derived dissolved organic matter is highly variable across seasons and habitats. Regression analysis was used to measure how bacteria covaried with algae in sea ice and water column habitats at three sites around Antarctica. Bacteria and algae were positively related in sea ice of the Weddell Sea during early winter 1992 (r2 = 0.16, slope = 0.24) and across sea ice and upper water column habitats of the Ross Sea during summer 1999 (r2 = 0.52, slope = 0.50). Conversely, bacteria and algae exhibited no discernible relationship in the water column and first year ice habitats of the Western Antarctic Peninsula region in winter 2001 (r2 = 0.003, slope = −0.04). Low algal production and residual biomass probably limited bacterial production and facilitated bacteria-algae uncoupling in winter sea ice of the Western Antarctic Peninsula. Winter sea ice algal biomass was probably limited by a relatively late date of initial ice formation, reduced multi-year ice coverage, and a lack of radiant energy in the winter ice pack.