Concerns exist regarding potential harms of community water fluoridation. The study objective was to examine the association between fluoride exposure and indicators of two health outcomes for which concerns have been expressed, cognitive and thyroid functioning, among a population-based sample of Canadians. Data were analyzed from Cycles 2 and 3 of the Canadian Health Measures Survey. Logistic regression and multinomial logistic regression were used to examine associations between fluoride exposure (from urine and tap water) and indicators of cognitive and thyroid functioning, adjusting for covariates. There was no evidence of any relationship between fluoride exposure and thyroid functioning. Higher urinary fluoride was associated with having some cognitive problems (versus none), but this finding disappeared when the sample was constrained to those for whom we could discern fluoride exposure from drinking water. Future research should continue to utilize this high quality data source to explore other potential harms.