Plant diversity and community structure can affect the abundance and diversity of belowground organisms. The McMurdo Dry Valley region lacks vascular plants, but several species of moss and algae occur at low density in and near aquatic habitats, such as ephemeral streams, and ice-covered lakes. The soil ecosystem supports a simple food web consisting of microbes, protozoa, nematodes, tardigrades and rotifers. We hypothesized that areas with a more productive community of vegetation (mosses and algae) will maintain a more abundant and diverse faunal community both aboveground and belowground. We characterized the invertebrate community along glacial streams and lakes which represent a gradient of primary productivity and habitat suitability. As predicted, there were significant differences in the nematode communities between soils collected beneath algal mats and those collected below mosses. Plectus spp., a bacterial feeder, dominated the algal soils, while Eudorylaimus spp., an algal feeder, was more abundant in moss soils. The most abundant and widely distributed nematode in the dry valleys, Scottnema lindsayae, a bacterial feeder that prefers dry soils, was not recovered from moss or algal soils. Animals were significantly more abundant in the vegetation than in the sediment directly beneath it, indicating a potential preference for aboveground habitats. Differences between collection sites were minimal; the soil community within the vegetated areas did not reflect the productivity gradient.