One of the fastest rates of recent climate warming has been reported for the Arctic and the maritime Antarctic; for example, mean annual temperatures increased by 0.5 °C per decade over the Antarctic Peninsula during the past 50 years. Owing to their comparatively simple and highly sensitive food webs, polar freshwater systems, with cyanobacterial mats representing the dominant benthic primary producers, seem well suited for monitoring environmental perturbation, including climate change. Prolonged climate change may challenge the resilience, plasticity and adaptability and thus affect the community composition of cyanobacterial mats. We demonstrate that exposing polar mat samples to raised temperatures for six months results in a change in species predominance. Mats exposed to a constant temperature of 8 °C or 16 °C showed high cyanobacterial diversity, commensurate with an increased presence of cyanobacterial toxins. In contrast, mats held at 4 °C and 23 °C seemed low in diversity. Our data thus indicate that a temperature shift to 8–16 °C, potentially reached during summer months in polar regions at the present warming rate, could affect cyanobacterial diversity, and in some instances result in a shift to toxin-producing species or to elevated toxin concentrations by pre-existing species that could profoundly alter freshwater polar ecosystems.