Exposure to bioaerosols has been implicated in adverse respiratory symptoms, infectious diseases, and bioterrorism. Although these particles have been measured within residential and occupational settings in multiple studies, the deposition of bioaerosol particles within the human respiratory system has been only minimally explored. This paper uses real-world environmental measurement data of total fungal spores using Air-o-Cell cassettes in 16 different apartments and residents’ physiological data in those apartments to predict respiratory deposition of the spores. The airborne spore concentrations were measured during the spring, summer, and fall. The respiratory deposition of five most prevalent spore genera—Ascospores, Aspergillus, Basidiospores, Cladosporium, and Myxomycetes—was predicted using three empirical models: the Multiple Path Particle Dosimetry model, using both the Yeh and age-specific versions, and the Bioaerosol Adaptation of the International Committee on Radiological Protection’s Lung deposition model. The predicted total deposited number of spores was highest for Ascospores and Cladosporium. While the majority of spores deposit were in the extrathoracic region, there is a significant deposition for both Aspergillus and Cladosporium in the alveolar region, potentially leading to the development of aspergillosis or allergic asthma. Although the dose–response relationship is unknown, the estimate of the actual spore deposition could be the first step in determining such a relationship.