Ambient air consists of bioaerosols that constitute many microbes from biosphere due to natural and anthropogenic activities. Size-dependent ambient measurements of bioaerosols at two seminatural and three anthropogenic coastal sites in southern tropical India were taken during the summer 2017. All the five sites considered in this study considerably contributed to the bioaerosol burden with larger contribution from the dumping yard site followed by the marshland site, wastewater treatment plant, composting site, and Indian Institute of Technology Madras. The colony-forming units concentration for all the sites ranged from 17 to 2750 m−3 for bacteria and 42–2673 m−3 for fungi. Firmicutes and Actinomycetes were the dominant phyla observed in 698 bacterial OTUs obtained, and Ascomycota and Zygomycota were the dominant phyla observed in 159 fungal OTUs obtained in the study. Further, the study revealed the presence of pathogenic and ice-nucleating bacteria and fungi in the bioaerosols that can largely affect the well-being of the human population and vegetation in this region. Moreover, the statistical analysis revealed high bacterial abundance and diversity at the grit chamber of wastewater treatment plant and high fungal abundance and diversity at the dumping yard. Further, principal coordinate analysis of the sites studied inferred that the marshland, wastewater treatment plant, and the dumping yard sites shared similar microbial community composition indicating the existence of similar source materials and activities at the sites. Further, this study evidently brings out the fact that urban locations may play an important role in anthropogenic contribution of both pathogenic and ice-nucleating microorganisms.