Wind blowing over aquatic and terrestrial surfaces produces aerosols, which include microbial aerosols. We studied the effect of onshore wind speeds on aerosol concentrations as well as total and culturable microbial aerosols (bacterial and viral) at an urban waterfront (New York, NY, USA). We used two distinct methods to characterize microbial aerosol responses to wind speed: A culture-based exposure-plate method measuring viable bacterial deposition near-shore (CFU accumulation rate); and a culture-independent aerosol sampler-based method measuring total bacterial and viral aerosols (cells m−3 air). While ambient coarse (>2 µm) and fine (0.3–2 µm) aerosol particle number concentrations (regulated indicators of air quality) decreased with increasing onshore wind speeds, total and depositing culturable bacterial aerosols and total viral aerosols increased. Taxonomic identification of the 16S rDNA of bacterial aerosol isolates suggested both terrestrial and aquatic sources. Wind appears to increase microbial aerosol number concentrations in the near-shore environment by onshore transport at low wind speeds (s−1 ), and increased local production and transport of new microbial aerosols from adjacent water surfaces at higher wind speeds (>4 m s−1 ). This study demonstrates a wind-modulated microbial connection between water and air in the coastal urban environment, with implications for public health management and urban microbial ecology.