Due to practical difficulties in quantifying fluoride exposure, the ability of various biomarkers to predict exposure has been investigated previously. However, the results are inadequate for validation of their application and usefulness. This study aimed to investigate the association between contemporary/recent biomarkers of fluoride exposure and total daily fluoride intake (TDFI) of children with large differences in fluoride exposure through drinking water. TDFI was assessed in 61 healthy 4-to 5-year-old children who provided at least 1 biomarker sample; 32 lived in a low-fluoride area (0.04 mg F/L) and 29 lived in a high-fluoride area (3.05 mg F/L). Validated questionnaires were administered to evaluate fluoride intake from diets (including water) and toothpaste ingestion. Daily urinary fluoride excretion (UFE) and fluoride concentrations in plasma, fasting whole saliva, hair, and nails (toenails/fingernails) were evaluated and related to total fluoride exposure. TDFI, UFE, and fluoride concentrations of biomarkers were statistically significantly higher in the high-fluoride area than in the low-fluoride area. There was a strong statistically significant positive correlation between TDFI and UFE (ρ = 0.756, p < 0.001); plasma fluoride concentration (ρ = 0.770, p < 0.001); and toenail fluoride concentration (ρ = 0.604, p < 0.001). The statistically significant positive correlation between TDFI and fingernail fluoride concentration (ρ = 470, p < 0.001) as well as between TDFI and fasting whole saliva fluoride concentration (ρ = 0.453, p = 0.001) was moderate, whereas it was weak between TDFI and hair fluoride concentration (ρ = 0.306, p = 0.027). In conclusion, the current study confirmed the suitability of 24-h urine samples for estimating fluoride exposure in children. The strong correlations between TDFI and fluoride in plasma and toenails also suggest these biomarkers may be considered for health risk assessments of fluoride in children who are susceptible to development of dental fluorosis.