Single-celled, eukaryotic microorganisms, known as protists, are responsible for 2 important, yet opposing, metabolic activities within aquatic food webs. They are major primary producers and highly active predators in marine and fresh water systems. While genomics has accelerated in recent years for this taxonomically diverse group, our understanding of the metabolic capabilities of most protists remains limited. It is also poorly understood how protist trophic mode is affected by biotic and abiotic factors, and therefore it is difficult to predict how events such as global climate change will affect the balance between autotrophic and heterotrophic activities in protist communities. To address open questions regarding how protist metabolic versatility is influenced by their environment, we characterized the potential for carbon fixation versus organic carbon degradation using enzymatic assays (RubisCO and β-D-glucosaminidase, respectively) within the water columns of ice-covered lakes in McMurdo Dry Valleys (MDV), Antarctica. Steep physical and chemical gradients in the water columns, microorganism domination and minimal allochthonous inputs makes the MDV lakes uniquely suited to investigate environment-microbe interactions. Spatial trends in RubisCO and β-D-glucosaminidase activities were lake-specific and vertically stratified within the water columns. Moreover, bottom-up drivers controlling the activity of C-fixation vs. organic C-degradation among the MDV protist communities were distinct between the upper photic vs. the deep, aphotic zones. We conclude that differential controls over major C-cycling enzymes have important implications on the influence of environmental change on the carbon and nutrient cycles in the MDV lakes.