Different types of non-extremophilic archaea have been detected in many different environments, ranging from terrestrial to marine and lacustrine ecosystems. The diversity, function and abundance of most of these, predominantly uncultured archaea is not yet clear. The methanogenic archaea are an exception, but also their functions and spatial and temporal distribution in freshwater environments is not well known. The methanogens have a considerable effect on factors affecting global climate change and many of the novel archaea have only recently been discovered to have influence on global biogeochemical cycles. This review will concentrate on freshwater ecosystems, emphasising the importance of the archaeal communities in freshwater.