Indoor air quality (IAQ) is impacted by polluted outdoor air in naturally ventilated schools, especially in places where both anthropogenic and natural sources of ambient air pollution exist. CO₂, PM_2.5, PM₁₀, temperature, relative humidity (RH), and noise were measured in five naturally ventilated primary schools in City of Sanliurfa, in a dusty region of Turkey, Southeast Anatolia. Excess risk levels were estimated for particulate matter. Investigation was conducted through an educational year including two seasons in terms of anthropogenic effect, that is, heating/non-heating, and natural effect, that is, desert dust transport/non-dust transport. The median CO₂ concentration was measured to be >1000 ppm in all seasons/schools. Temperature and RH fell out of the comfort zone in October–December, during which pollutant concentrations were considerably increased, specifically in November, that heating and dust transport periods coincide. The overall mean indoor PM₁₀ and PM_2.5 levels were 58 and 31.8 μg/m³, respectively. Risk assessment indicate that both short (incidence of asthma symptoms in asthmatic children) and long-term (prevalence of bronchitis) effects are considerable with 10.9 (2.4–19.6)% and 19.5 (2.2–38.8)%, respectively. The findings suggest that mechanical ventilation retrofitting with particle filtration is needed to mitigate potential negative health consequences on children.