IntroductionWater fluoridation is an effective measure to prevent dental caries. In Japan, artificial water fluoridation is not implemented, and tap water natural fluoride concentration geographically differs because of various soil natures. This study aimed to examine the association between tap water natural fluoride and parent‐reported experience of dental caries in children.MethodData from the Longitudinal Survey of Newborns in the twenty‐first century, a national birth cohort study following all infants born between January 10–17 and July 10–17, 2001, were analysed. Caregivers answered the child's caries treatment history, a proxy for dental caries, yearly from 5.5 to 12 years of age (N = 202 517 observations from 34 998 children). The annual data on tap water natural fluoride concentration in the municipality of residence were obtained from the national statistics. Cross‐classified multilevel Poisson regression models were fitted, adjusting for child, household and municipality characteristics, including average income and dental clinic density.ResultsThe average tap water natural fluoride concentration across municipalities was 0.0887 ppm (SD = 0.0422). The proportion of parent‐reported experience of child dental caries treatment ranged from 24.9% (at 12 years) to 40.3% (at 7 years) and was lower among children living in municipalities with high natural fluoride concentrations, which were 35.0%, 35.4%, 33.4% and 32.3% for <0.10, 0.10–0.19, 0.20–0.29 and ≥0.30 ppm respectively. A 0.1 ppm increment in tap water natural fluoride after controlling for all covariates was significantly associated with a lower prevalence of parent‐reported child dental caries treatment by 3.3% (prevalence ratio = 0.967, 95% credible interval: 0.939, 0.996).ConclusionNatural fluoride in tap water showed a protective effect for the parent‐reported experience of child dental caries in Japan.