The aim of this thesis was to understand variation in microbial aerosol (or bioaerosol) communities at differing spatial and temporal scales. Bioaerosols in urban parks were shown to vary as a result of location, sampled air-mass source and, for fungi in particular, time. Modelling was able to explain 38% of the fungal variation and 19% of the bacterial variation. Urban sampling over two years confirmed that bioaerosol communities varied over time in a non-linear fashion, exhibiting marked seasonality, which was especially pronounced for fungi. Non-linear diel variation was detected for Antarctic fungi. Bacteria in common between Antarctica and New Zealand increased markedly when New Zealand air was coming from Antarctica, suggesting intercontinental transport for bacteria at notable rates. Fungi appeared to undergo much less long-range atmospheric transport. This thesis research contributes innovative, validated data collection and processing pipelines for sparse microbial community data to our body of information. Novel patterns in bioaerosol spatiotemporal variation have been revealed that lead to new questions about bioaerosol community structure and ecosystem connectivity via bioaerosols. As understanding of the drivers of bioaerosol variation improves, predictions can be made regarding future ecosystem changes and spread of infectious microorganisms. This will be crucial for managing the impacts of these increasingly likely events in the face of climate change.