Microorganisms are ubiquitous in their distributions and are integral to global nutrient cycling. Yet, microbial metabolic strategies are niche-specific, as environmental conditions including nutrient and moisture availability, oxygen concentration, and salinity select for certain microbial adaptations. The Salton Sea, a hypersaline and eutrophic lake in Southern California, presents a unique opportunity to investigate how the environment selects for microbial survival and dispersal, which has urgent implications for both ecosystem stability and public health impacts. In Chapter 1, we explored the geochemistry of the Salton Sea sub-ecosystems (i.e., the playa, seawater, and aeolian) and how they structure their respective microbiomes. We also detail the paucity of research into these communities and describe modern methods like metagenomics and wind modeling that could be used to characterize the Salton Sea microbiomes. In Chapter 2, we examined the Salton Seawater microbiome within a water column during periods of lake stratification and turnover in 2020 and 2021. We characterized the taxonomic composition of the lake’s microbiome across seasons by sequencing the bacterial 16S rRNA gene (V3-V4) and used metagenomic sequencing to assess the community’s capacity for sulfur cycling. While microbiome composition significantly varied between seasons, halophilic, mixotrophic bacteria consistently dominated the water column. Additionally, sulfur oxidation genes were shared across depths and their relative coverage fluctuated with seasonal shifts in oxygen, sulfide, and sulfate concentrations. In Chapter 3, we used amplicon sequencing of the 16S rRNA gene (V3-V4), metagenomic sequencing, and wind geospatial data to characterize the aeolian dust microbiome and their adaptations that permit atmospheric survival and dispersal. We identified a core aeolian microbiome including bacterial genera such as Massilia, Sphingomonas, and 11 other stress-tolerant taxa. We also observed that the dust microbiome contains the necessary adaptations for persisting in dust, including UV radiation resistance genes and osmotic resistance genes, and that the distribution of these traits was driven by wind conditions. Together, these findings demonstrate that harsh environments select for microbial survival strategies, which in turn, regulate the ecosystems’ geochemistry and stability. Furthermore, this relationship structures both microbial colonization and dispersal, which may pose a danger to the public upon exposure.