Colonization of remote ecosystems by new microorganisms poses a significant threat to the diversity and function of native microbial communities. In the polar regions, including Antarctica, airborne microbial communities are shaped by environmental and climatic factors, which are changing rapidly. However, the specific drivers of microbial community composition and diversity in these regions remain poorly understood. This study explores the daily dynamics of airborne bacterial communities over South Georgia, a large and remote sub-Antarctic Island, and evaluates the influence of environmental factors, local microbiomes, and sampling methodology. Over two weeks, near-surface air samples were collected from coastal and higher-altitude (200 m a.s.l) sites using different air samplers. The Coriolis Compact sampler, run for longer durations, captured higher diversity, while the Coriolis Micro provided high-quality snapshots during shorter sampling windows. Results showed rapid daily turnover in community composition (up to 90%) alongside a stable core microbiome (10–20%). Coastal microbial communities were shaped by local microbiomes, especially wildlife-associated taxa, whereas high-altitude communities were more variable, suggesting influence from long-range microbial dispersal. Environmental factors, including wind direction, temperature, and rainfall, also significantly shaped community structure. These findings highlight the dynamic nature of airborne microbiomes in the sub-Antarctic.