This study aimed at determining culturable airborne bacteria (CAB) and fungi (CAF) concentrations in different sections of a primary school located in Istanbul. Occupancy variables were determinants of exposure and the environmental, ventilation, and comfort parameters within the study. Air samples were collected twice in the summer and spring seasons using a microbial air sampler (Sampl’air™) and were analyzed in terms of CAB and CAF concentrations. Obtained results were visualized using geographic information system (GIS) technology for presenting the spatial variations of CAB and CAF concentrations with respect to environmental determinants and changing weather conditions as temperature and humidity. The study introduced that the CAB and CAF concentrations vary indoors based on the sampling location and human occupancy. As an interesting finding of the study, CAB (3300 CFU/m3) and CAF (3100 CFU/m3) concentrations in the 5th classroom, where relative humidity and temperature values were recorded as 62% and 25.3 °C, respectively, were observed, confirming higher values than those of communal areas. This result proved the importance of indoor characteristics like location, ventilation, occupation time, and hygiene as the substantial determinants of CAB and CAF exposure besides the indoor population. This study emphasized the importance of regular and systematic monitoring of airborne microorganisms in different sections of schools using objective and quantitative methodologies in terms of providing healthy educational environments for students.