Community water fluoridation (CWF) is a measure of recognized importance due to its effectiveness in preventing tooth decay at the population level. However, for the maximum benefit to be achieved, the high-quality standard of CWF must be maintained over time. To analyze the municipality-level characteristics associated with quality of water fluoridation in São Paulo state, Brazil. An ecological study was performed using official data sources on fluoride concentration surveillance in 2015. The outcome was municipalities that have not met the quality standard, identified as those with less than 80% of water samples within the optimal level for caries prevention. The independent variables were municipality-level indicators related to demographics, economics, and sanitation characteristics. Crude and adjusted prevalence ratios were estimated using Poisson regression with robust variance. In total, 43.4% municipalities exhibited the outcome. Adjusted by Gini index, the prevalence ratio was 32% higher in municipalities with lower annual gross domestic product per capita. Adjusted by social responsibility index and earlier variables, the prevalence was higher in the municipalities with higher per capita expenditure on sanitation and health surveillance, where the urban population rate was lower, and with a human development index ≤0.761. Adjusted by earlier variables, the prevalence ratio was twice and 3.5 times higher for municipalities, respectively, with per capita income less than or equal to US$574 and where the type of sanitation utility was municipal and private; 50% higher in those with less than 100,000 habitants; and 20% higher in those with a chlorine concentration nonconformity rate above 0.82%. To ensure high quality of CWF, additional management measures should be implemented in municipalities with less than 100,000 habitants, a higher chlorine concentration nonconformity rate, a lower per capita income, and where the type of sanitation utility was municipal or private. The study showed that the quality of fluoridation was associated with municipality-level characteristics. The findings can be used by policy makers to identify and support municipalities that will need to improve fluoridation quality if they are to reach oral health goals.