Considerable attention is now focused on permafrost systems given the accelerated warming of the Arctic and the potential mobilization of its vast stocks of soil organic carbon, and the wide-ranging importance of permafrost for geosystem and ecosystem processes throughout the polar regions. Although many terrestrial studies have provided new information about permafrost degradation and its associated carbon dynamics, few have considered the role of aquatic ecosystems in these processes. There has been little consideration given to the strikingly diverse and changing limnology of these lake and river systems, including their geomorphology, hydrology, hydrodynamics, other physical and ecosystem properties, biogeochemistry, biodiversity and food webs, microbiology, photochemistry and regional differences. More knowledge about each of these aspects is needed for a full understanding of the global importance of thaw aquatic ecosystems as biogeochemical reactors; as elemental sources, sinks and conduits; as ecological oases in the Arctic and Antarctica; and as systems that may respond rapidly to climate change. This special issue brings together specialists from different disciplines to share their knowledge about these dynamic systems on permafrost landscapes, and to identify priorities for future research.