Microorganisms are the most diverse life form on the planet and are critical for maintaining geochemical cycles in extreme environments. This study examined microbial community diversity in Salar de Huasco, a high-altitude poly-extreme wetland, to determine whether diversity and composition changed in response to geographical and seasonal variations. Analysis revealed significant differences in bacterial diversity, abundance, and composition that could be attributed to local geographical and seasonal variations. In this poly-extreme environment, small-scale changes trigger significant changes in microbial communities that maintain basic biogeochemical cycles.