Polar regions are warming more rapidly than lower latitudes, and climate models predict that this trend will continue into the coming decades. Despite these observations and predictions, relatively little is known about how polar ecosystems have responded and will continue to respond to this change. Two Long-Term Ecological Research (LTER) sites, located in contrasting environments in Antarctica, have been studying marine and aquatic terrestrial ecosystems for more than two decades. We use data from these research areas to show that the extent and thickness of ice covers are highly sensitive to short- and long-term climate variation and that this variation significantly influences ecosystem processes in these respective environments. Declining sea-ice extent and duration diminishes phytoplankton blooms as a consequence of reduced water stratification, whereas the thinning of lake-ice cover enhances phytoplankton blooms because of increased penetrating light into the water column. Both responses have cascading effects on upper trophic levels.