Polar regions have been identiWed as being most sensitive to climate warming in the planet. The Arctic is experiencing the highest warming on Earth with air temperature increasing at a rate of two to three times that of the global average temperature (International Panel on Climate Change 2007). Atmospheric warming has increased Arctic Ocean temperature and accelerated ice melting, with sea ice decreasing in thickness and extent at a rate of 10% per decade (Comiso et al. 2008). Warming and the associated ice loss appears to have been accelerating in the past few years in the Arctic and in some regions of Antarctica as well (Steig et al. 2009). The Arctic Ocean experienced a massive loss of ice in the summer of 2007, representing the lowest ice cover in the last 40 years, and an unusually warm Arctic Ocean surface layer were recorded (Steele et al. 2008; Zhang et al. 2008). Provided the critical role of ice cover in determining the functioning and traits of polar marine and freshwater ecosystems, rapid ice loss is expected to severely impact these ecosystems at multiple levels. The impact of warming and ice loss will aVect, in turn, the radiative balance of polar waters, aVecting their thermal and light, including UV, environments. Recent overviews of results from observational studies of atmospheric and climate-sensitive variables (e.g., sea ice, snow cover, river discharge, glaciers and permafrost) concluded that, taken together, a reasonably coherent portrait of recent change in the northern high latitudes is apparent. Ice loss will intensify air–water interactions in polar ecosystems and will also severely impact all species, from microbes to megafauna, that depend on ice as a habitat. Warming and ice loss will aVect key biological and biogeochemical processes of aquatic polar ecosystems and may induce ecological regime shifts, associated with possible losses of biodiversity and an increased vulnerability to invasions of species from lower latitudes. The goal of this special issue is to bring together recent research results addressing impacts of warming and ice loss in both Antarctic and Arctic aquatic ecosystems. “Impacts of Climate Warming on Polar Marine and Freshwater Ecosystems” was the title of a topical session of the Aquatic Science Meeting of the American Association of Limnology and Oceanography (ASLO), held in Nice (France) from 23 to 30 January 2009, during which results from both benthic and pelagic, freshwater and marine polar ecosystems were presented. Susana Agusti and Mikael K. Sejr acted as Chairs of this ASLO session, which received Wnancial support by the Prince Albert II of Monaco Foundation. Some papers presented in the session are published in this special issue of Polar Biology. Results from Antarctic aquatic ecosystems presented in this special issue highlight the temporal variability of marine and freshwater systems of the Antarctic Peninsula in the west of the continent, which is the region experiencing the strongest warming (Steig et al. 2009). The signiWcant increase in temperature across most of West Antarctica, exceeding 0.1°C per decade over the past 50 years, is attributed to global warming and to the increased strength of the circumpolar westerlies in response S. Agusti (&) · C. M. Duarte Department of Global Change Research, Instituto Mediterraneo de Estudios Avanzados IMEDEA, CSIC–UIB, Mallorca, Spain e-mail: sagusti@imedea.uib-csic.es