The planktonic microbial communities of three meltwater ponds, located on the McMurdo Ice Shelf, were investigated from the end of January 2008 to early April, during which almost the entire pond volumes froze. The ponds were comprised of an upper mixed layer overlying a salt-stabilized density gradient in which planktonic communities were primarily embedded. Plankton comprised all components of the “microbial loop”, though carnivorous protists were rare. As the ponds froze and light became increasingly limited, it was expected conditions would induce physiological changes altering the functional role of autotrophic and heterotrophic microplankton within the ponds. The results showed that microbial groups responded to the onset of winter by declining in abundance, though an exception was the appearance of filamentous cyanobacteria in the water column in March. As freezing progressed, autotrophs declined more rapidly than heterotrophs and grazing rates and abundances of mixotrophic and heterotrophic organisms increased. Grazing pressure on bacteria and picophytoplankton also increased, in part explaining their decline over time. The results indicate that stressors imposed during freezing select for increasing heterotrophy within the remaining microbial communities, although all components of the food web eventually decline as the final freeze approaches.