The Palmer and McMurdo LTER (Long Term Ecological Research) sites represent climatic and trophic extremes on the Antarctic continent. Despite these differences, the microbial components of the McMurdo lake and Palmer marine ecosystems share fundamental characteristics, including the production of organic carbon via autotrophy and its assimilation via heterotrophy. We leveraged 20+ years of observations at the Palmer and McMurdo LTERs to identify key differences in microbial ecosystem dynamics between these sites. Although the relationships between fundamental biological parameters, including autotrophy and heterotrophy, are different between these sites, recent climate events have influenced the coupling of these parameters. We hypothesize that for the lakes of the McMurdo LTER, decoupling is largely driven by physical processes, whereas in the coastal Antarctic, it is largely driven by biological processes. We combined this hypothesis with a new analysis of microbial community and metabolic structure to develop novel conceptual microbial food-web models.