Climate change is occurring globally, with wide ranging impacts on organisms and ecosystems alike. While most studies focus on increases in mean temperatures and changes in precipitation, there is growing evidence that an increase in extreme events may be particularly important to altering ecosystem structure and function. During extreme events organisms encounter environmental conditions well beyond the range normally experienced. Such conditions may cause rapid changes in community composition and ecosystem states. We present the impact of an extreme pulse event (a flood) on soil communities in an Antarctic polar desert. Taylor Valley, McMurdo Dry Valleys, is dominated by large expanses of dry, saline soils. During the austral summer, melting of glaciers, snow patches and subsurface ice supplies water to ephemeral streams and wetlands. We show how the activation of a non-annual ephemeral stream, Wormherder Creek, and the associated wetland during an exceptional high-flow event alters soil properties and communities. The flow of water increased soil water availability and decreased salinity within the wetted zone compared with the surrounding dry soils. We propose that periodic leaching of salts from flooding reduces soil osmotic stress to levels that are more favorable for soil organisms, improving the habitat suitability, which has a strong positive effect on soil animal abundance and diversity. Moreover, we found that communities differentiated along a soil moisture gradient and that overland water flow created greater connectivity within the landscape, and is expected to promote soil faunal dispersal. Thus, floods can ‘precondition' soils to support belowground communities by creating conditions below or above key environmental thresholds. We conclude that pulse events can have significant long-term impacts on soil habitat suitability, and knowledge of pulse events is essential for understanding the present distribution and functioning of communities in soil ecosystems.