Environmental exposure of preschool children to mercury can elevate blood mercury levels (BML) and negatively affect their health. This study aimed to determine BML in preschool children from Brazil's largest city and explore potential associated risk factors. Blood samples were collected in 2013 from 2436 children (age 1–5 years) attending 50 daycare centers (DCC) located in São Paulo, Brazil. Parents or guardians answered questionnaires collecting information on sociodemographics and potential risk factors. BML was determined by Cold Vapor Atomic Absorption Spectrophotometry (CV-AAS) and categorized using a cutoff point of 2.77 μg L⁻1, corresponding to the 75th percentile. Multiple logistic regression was performed (p < 0.05). Data were georeferenced and associations with air pollution, wind frequency and direction were evaluated. The results showed a geometric mean for BML of 1.65 μg L⁻1 (95% CI: 1.60–1.70), arithmetic mean of 2.15 μg L⁻1 (95% CI: 2.09–2.22), 75th percentile of 2.77 μg L⁻1 (95% CI: 2.67–2.91) and 95th percentile of 5.51 μg L⁻1 (95% CI: 5.18–5.92). DCCs located in the Northwest and East zones (p < 0.001) and fish consumption in the past two days (p = 0.04) were associated with high BML. The elevated BML observed in children living in the eastern zone might be attributed to the southeasterly winds passing through a petrochemical complex located nearby. The 95th percentile of BML in this study exceeded the U.S. 95th percentile by five times. BML in São Paulo preschool children was associated with individual and environmental risk factors. This finding highlights the need to identify and control hot spots in São Paulo, Brazil, especially in peripheral and surrounding areas, where individuals are more vulnerable. Further research is needed in Latin America to identify additional sources of urban environmental mercury exposure and guide interventions for protecting the environment and safeguarding children's health.