<p>Antarctic lakes are extreme, oligotrophic habitats that contain microbial communities distinct from those of temperate freshwater systems. Our central question was whether these lakes host microbial communities distinct from those of non-Antarctic freshwater systems, and how environmental variability drives community differences among Antarctic lakes themselves. We analyzed the microbial community across five lakes on King George Island via high-throughput sequencing of amplicon sequence variants (ASVs) and biogeochemical profiling. The microbial communities were dominated by Bacteroidota, Actinomycetota, and Pseudomonadota, but varied strongly with environmental gradients such as salinity, sulfate, methane, and organic carbon. Hybrid ASVs, which were ubiquitous in both water and sediment, comprised the majority of sequences and indicate that dispersal processes, alongside environmental filtering, jointly structure lake microbial communities. Functional predictions further revealed lake- and habitat-specific pathways for carbon, nitrogen, and sulfur cycling, linking microbial diversity to ecosystem processes. These findings highlight how Antarctic lake microbes are shaped by both local selective pressures and cross-habitat exchange, providing critical insights into the resilience and vulnerability of polar freshwater ecosystems under climate change.</p>