The daily deposited dose of bioaerosols and particle mass or number in the human respiratory tract using an exposure dose model (ExDoM2) was quantified in the present study. The dose was calculated for the extrathoracic (ET), tracheobronchial (TB), and alveolar-interstitial (AI) regions of the human respiratory tract. The calculations were performed for viable, cultivable airborne heterotrophic bacteria, mesophilic fast-growing fungi, and total coliforms at a municipal wastewater treatment plant (WWTP) located at a suburban area at a Mediterranean site. The human dose was determined using data from two locations at the WWTP which correspond to two different wastewater treatment stages (aerated grit chamber (indoor) and primary settling tanks (outdoor)) and one outdoor location at the urban background site. In addition, the model simulations were performed for two exposure periods (March to April and May to June 2008). Higher daily deposited dose in the total human respiratory tract was observed for heterotrophic bacteria at the aerated grit chamber, whereas lower values of heterotrophic bacteria were observed at the primary settling tanks. These findings were associated with the corresponding stage of wastewater treatment activities and may be valuable information for determining future dose–response relationships. In addition, higher daily deposited dose was determined in the ET region for the three categories of bioaerosols. Regarding PM10 and PN1, the higher daily deposited dose received by a worker at the aerated grit chamber. Finally, the hazard quotients were estimated and the results showed that the non-carcinogenic effects can be ignored for bioaerosols and PM10 except for workers present at aerated grit chamber. Regarding PM2.5, the non-carcinogenic effects are of concern and cannot be ignored for all cases.