Aerobiology is rapidly expanding as airborne environmental DNA (eDNA) enables ecosystem-scale monitoring, yet key uncertainties remain regarding transport, persistence, and interpretation of airborne communities. Here, we integrate relative and absolute abundance measurements across five biological kingdoms in a high-frequency, four-month urban time series. This combined framework allows us to disentangle changes in community composition from shifts in total biomass—an important but often overlooked distinction. We find that bacterial communities exhibit local filtering, contrasting with other clades that show greater evidence of regional transport. Across kingdoms, meteorological variables—particularly precipitation, temperature, and wind—consistently shape both community structure and total abundance, but with clade-specific responses. Notably, community turnover and abundance are partially decoupled, indicating distinct ecological and physical controls on airborne biodiversity. These results provide empirical insight into a central challenge in airborne eDNA research: distinguishing local ecological signals from transported material. By combining multi-kingdom resolution with absolute quantification, this study advances the interpretation of aerobiome data and highlights the importance of integrating ecological and atmospheric processes in understanding airborne life.