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We studied invertebrate communities across a transition zone between soils and stream sediments in the cold desert landscape: of Taylor Valley, Antarctica. We hypothesized that hydrological and biogeochemical linkages in the functionally important transition zone between streams and surrounding soils should be important in structuring invertebrate communities. We compared invertebrate communities along transects beginning in the saturated sediments under flowing stream water and extending laterally through the hyporheic zone to the dry soils that characterize most of the dry valley landscape. Nematodes, rotifers, and tardigrades assembled into different communities in soils and sediments, but there was no relationship between the total abundance of invertebrates and moisture. Community diversity was, however, influenced by the moisture and salinity gradients created with distance from flowing waters. The wet, low-salinity sediments in the center of the stream contained the most invertebrates and had the highest taxonomic diversity. Adjacent to the stream, communities in the hyporheic zone were influenced strongly by salt deposition. Abundance of invertebrates was low in the hyporheic zone, but this area, contained the most co-occurring nematode species (three species). In dry seas, communities were composed almost entirely of a single species of nematode, Scottnema lindsayae, an organism not found in the stream center. These results suggest spatially-partitioned niches for invertebrates in soils and sediments in the dry valley landscape based on proximity to sources of moisture and the interactive effects of salinity.