Passive sampling methodology was applied to collect particulate matter (PM) in classrooms of urban and rural primary schools. The samples were taken during a year by passive deposition allowing the study of seasonal variability of the particles masses and chemical content. Chemical characterization of the collected particles was performed in order to measure its soluble ions content and elemental composition. To identify the main polluting sources, correlations between parameters and enrichment factors were studied. Higher particle masses concentrations were registered in autumn, with a mean of 1.54 ± 0.74 μg day−1 cm−2. The major element in the collected particles was calcium, representing 63–73% of the analyzed mass of the particles inside the urban classrooms. In the rural cluster, calcium remained the major component but with a slight lower contribution to the overall particles composition (42–46%). The calcium source was hypothesized to be the chalk used in the blackboards of the classrooms due to a strong correlation found between Ca2+ and SO42−. Soil re-suspension, traffic and other anthropogenic emission sources were also identified. Analysis showed enrichment of the particles with Br, Ca, Zn and Sb in the urban cluster and enrichment of the same elements, except for Ca, in the rural cluster. The comparison between the results from both clusters allowed the identification of classrooms with higher particles concentrations that can indicate potential indoor air quality problems (reflected by an indoor accumulation of pollutants).