In this review we consider the physical processes that shape inland aquatic ecosystems and how these affect ecosystem processes, with particular focus on the nitrogen cycle. Inland Antarctica is dominated by microbial communities that are usually concentrated in, or adjacent to, habitats with free water. The presence of free vs frozen water is dependent on very small changes in temperature around 0°C, so significant variability in the distribution of free water can be expected in response to variations in climate over diel, decadal, to millennial time scales and a range of spatial scales. Antarctic inland waters take many forms: snow-surface melt pockets, cryoconites, basal regions of wet-based glaciers, ponds (varying in salinity and degree of desiccation), melt streams, perennially and seasonally ice covered lakes and even hypersaline, ice free lakes. The important processes and transformations that characterize the nitrogen cycle worldwide have all been identified in Antarctic inland waters and in some cases (e.g. N-uptake, N-fixation), rates are similar to those at lower latitudes. The unique features of Antarctic ecosystems stem from the extreme and variable physical conditions under which these processes operate rather than any unique ecosystem processes per se.