Arctic freshwater systems experience a short ice-free season and are therefore often oligotrophic, with food webs that largely rely on energy subsidies from the terrestrial surroundings. As a result, a large proportion of microorganisms – including archaea – originating from the surrounding soils, seem to find their way into the freshwater lakes (Crump et al. 2012). There also seems to be little transport of freshwater archaea into the Arctic Ocean, as almost no shared taxa are found between large freshwater rivers such as the Mackenzie River and the adjacent coastal ocean (Galand et al. 2006).

Notable differences between such low- and high-salinity environments were an almost complete absence of Nitrososphaerota in the freshwater biome, while this phylum was dominant in oceanic systems. Diverse Euryarchaeota were recovered both from the freshwater and the coastal ocean, but with phylogenetically distinct taxa in each (Galand et al. 2006, Gantner et al. 2011). Local conditions and chemical gradients are important in shaping the archaeal microflora in Arctic lakes.  A good example are the Arctic meromictic systems, where some water layers do not – or only occasionally – intermix. As a result, those systems often develop strong chemical gradients, with more saline bottom waters that become anoxic. Analogously to the more extensively studied meromictic lakes in Antarctica (Lauro et al., 2011) Arctic meromictic lakes also feature unique archaeal communities that are strongly stratified along depth and the associated chemical gradients (Pouliot et al., 2009).