Atmospheric bioaerosols contain live and dead biological components that can enter the human respiratory tract (HRT) and affect human health. Here, the total microorganisms in a coastal megacity, Qingdao, were characterized on the basis of long-term observations from October 2013 to January 2021. Particular attention was given to the size dependence of inhalable bioaerosols in concentration and respiratory deposition in different populations on foggy and hazy days. Bioaerosol samples stained with 4,6-diamidino-2-phenylindole (DAPI) were selected to measure the total airborne microbe (TAM) concentrations with an epifluorescence microscope, while a multiple-path particle dosimetry model was employed to calculate respiratory deposition. The mean TAM concentrations in the particle size range of 0.65–1.1 μm (TAM₀.₆₅–₁.₁) were 1.23, 2.02, 1.60 and 2.33 times those on sunny reference days relative to the corresponding values on days with slight, mild, moderate and severe levels of haze, respectively. The mean concentration of TAMs in the particle size range of 0.65–2.1 μm (TAM₀.₆₅–₂.₁) on severely hazy days was (2.02 ± 3.28) × 10⁵ cells/m³, with a reduction of 4.16% relative to that on the reference days. The mean TAM₀.₆₅–₂.₁ concentration changed from (1.50 ± 1.37) × 10⁵ cells/m³ to (1.76 ± 1.36) × 10⁵ cells/m³, with TAM₀.₆₅–₁.₁ increasing from (7.91 ± 7.97) × 10⁴ cells/m³ to (1.76 ± 1.33) × 10⁵ cells/m³ on days with light fog days and medium fog, respectively. The modeling results showed that the majority of TAM₀.₆₅–₂.₁ deposition occurred in the extrathoracic (ET) region, followed by the alveolar (AL) region. When different populations were examined separately, the deposition doses (DDs) in adult females and in children ranked at the minimum value (6.19 × 10³ cells/h) and maximum value (1.08 × 10⁴ cells/h), respectively. However, the inhalation risks on polluted days, such as hazy, foggy and mixed hazy–foggy (HF) days, were still below the threshold for adverse impacts on human health.