Changes in climate and ultraviolet radiation levels in the Arctic will have far-reaching impacts, affecting aquatic species at various trophic levels, the physical and chemical environment that makes up their habitat, and the processes that act on and within freshwater ecosystems. Interactions of climatic variables, such as temperature and precipitation, with freshwater ecosystems are highly complex and can propagate through the ecosystem in ways that are difficult to project. This is partly due to a poor understanding of arctic freshwater systems and their basic interrelationships with climate and other environmental variables, and partly due to a paucity of long-term freshwater monitoring sites and integrated hydro-ecological research programs in the Arctic. The papers in this special issue are an abstraction of the analyses performed by 25 international experts and their associated networks on Arctic freshwater hydrology and related aquatic ecosystems that was initially published by the Arctic Climate Impact Assessment (ACIA) in 2005 as "Chapter 8--Freshwater Ecosystems and Fisheries". The papers provide a broad overview of the general hydrological and ecological features of the various freshwater ecosystems in the Arctic, including descriptions of each ACIA region, followed by a review of historical changes in freshwater systems during the Holocene. This is followed by an assessment of the effects of climate change on broad-scale hydro-ecology; aquatic biota and ecosystem structure and function; and arctic fish and fisheries. Potential synergistic and cumulative effects are also discussed, as are the roles of ultraviolet radiation and contaminants. The nature and complexity of many of the effects are illustrated using case studies from around the circumpolar north, together with a discussion of important threshold responses (i.e., those that produce stepwise and/or nonlinear effects). The issue concludes with summary the key findings, a list of gaps in scientific understanding, and policy-related recommendations.