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Critical transition zones, such as aquatic-terrestrial interfaces, have been recognized as important features in landscape ecology. Yet changes in the community structure of soil and sediment biota across aquatic-terrestrial boundaries remain relatively unstudied. We investigated the community structure of the dominant fauna, namely nematodes, rotifers and tardigrades, across lake sediment-soil transects in three basins in a species-poor, polar desert ecosystem (McMurdo Dry Valleys, Antarctica). We also examined substrate (that is, soil and sediment) properties, including moisture, salinity, carbon, nitrogen and phosphate concentration, across these transects. Differences in faunal community structure and biochemical properties were typically explained by hydrologic basin and the sediment-soil gradient, but not by transects within each basin. Bonney Basin contained the least organic carbon, chlorophyll a, nematodes and taxa, whereas there was little difference in many of these measures between Fryxell and Hoare Basins. Nematode (Scottnema lindsayae and Plectus sp.) and rotifer abundance varied along sediment-soil transects. Scottnema lindsayae, the most abundant and widely distributed soil animal in this ecosystem, increased in abundance from sediments to soils, whereas Plectus sp. and rotifer abundance, and taxa richness (that is, nematodes, rotifers and/or tardigrades), decreased; Eudorylaimus sp. and tardigrade abundance did not differ significantly along the transects. Previous studies of soil biodiversity and faunal abundance in this ecosystem have revealed a positive association between these measures and biogeochemistry, if this holds true for lake sediments, our findings suggest sediments in Lake Bonney experience lower rates of nutrient cycling than either Lakes Fryxell or Hoare. Despite differences in faunal abundances along the sediment-soil transects, taxa occurrence was surprisingly similar in soil and sediment, only S. lindsayae was restricted to soil or the lake shore. In contrast, in other ecosystems, soil community composition differs greatly from lake sediments, suggesting that the observed similarity in species occurrence in both soils and sediments may be unique to Antarctica. This finding might result from the extreme low diversity of this ecosystem, presumably limiting competition among fauna, and thus promoting broad ecological niches. Alternatively, environmental conditions in Antarctica may select for species with broad ecological niches.