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San Juan del Río occupies a strategic position in central Mexico's Querétaro state, situated at approximately 1,920 meters above sea level in the Trans-Mexican Volcanic Belt's southern foothills. This mid-sized city lies along the historic Camino Real de Tierra Adentro, connecting Mexico City to northern mining regions, which historically shaped its urban character as a commercial and transportation hub. The city spreads across the San Juan River valley, with the river itself flowing northwest to southeast through the urban core, providing limited natural ventilation. Surrounding terrain features rolling hills to the east and west that can trap pollutants, while the broader region transitions from urban zones to extensive agricultural lands growing maize, beans, and alfalfa. San Juan del Río's location within Querétaro's industrial corridor—particularly its proximity to automotive and manufacturing facilities in nearby El Marqués and Corregidora—creates a complex urban-rural gradient where industrial emissions mix with agricultural dust and urban vehicle exhaust. The city's position approximately 130 kilometers northwest of Mexico City places it downwind of the megalopolis during certain seasonal patterns, though local topography and elevation moderate some regional pollution transport. Limited green spaces within the urban fabric and ongoing suburban expansion contribute to heat island effects that can exacerbate ozone formation during warm periods.

San Juan del Río experiences distinct seasonal air quality patterns shaped by its highland subtropical climate. During the dry winter months from December to February, cool temperatures and frequent temperature inversions trap pollutants close to the valley floor, particularly overnight and early morning when calm winds prevail. This period sees elevated particulate matter from increased residential heating and agricultural burning in surrounding fields. Spring (March-May) brings warmer temperatures and stronger daytime winds that disperse pollutants, though occasional dust storms from dry agricultural lands can temporarily degrade air quality. The summer rainy season (June-September) provides natural cleansing through afternoon thunderstorms that wash particulate matter from the air, creating the year's best conditions for outdoor activities—particularly July and August when rainfall peaks. However, high humidity combined with industrial and vehicle emissions can occasionally produce ground-level ozone on hot, stagnant days before storms develop. Autumn (October-November) marks a transition period where decreasing rainfall and increasing agricultural burning lead to gradual pollution buildup. Sensitive groups including children, elderly residents, and those with respiratory conditions should limit strenuous outdoor activities during winter mornings and late autumn afternoons when pollution concentrations typically peak. The most favorable months for outdoor recreation are generally July through September when rainfall maximizes natural ventilation.