Fluoride concentrations of 0.5 mg/L in drinking water are considered useful for dental caries prevention. However, fluoride concentrations higher than 1.2 mg/L in water can pose a risk of dental fluorosis due to high exposure to fluoride. The objective is to determine the fluoride concentration in water from aqueducts of different Colombian municipalities of Cauca (Popayán, Coconuco, and Puracé) to assess the fluoride dietary intake from the consumption of this water. A total of 66 water samples have been taken from Popayán, Coconuco, and Puracé. Fluoride content was determined by fluoride ion-selective electrode (ISE) potentiometry. The fluoride concentrations recorded in Coconuco and Puracé water were ≤ 0.002 mg/L. The mean fluoride content recorded in the Popayán water was 0.42 mg/L, with its highest concentration in Cauca River water (0.83 mg/L). Considering the admissible intake values, the water from Popayán confers remarkable fluoride intakes, especially in children with high percentages of contribution to the admissible daily intake (46.7% to 7- to 12-month children and 41.5% to 1- to 3-year children). The fluoride content in the water of Coconuco and Puracé does not reach an optimal value (< 0.5 mg/L) for the protective effect against dental caries, while the water of the main Cauca River basin does reach the optimal value. Likewise, the intake of fluoride from the consumption of the analyzed water does not confer any health risk. However, the implementation of monitoring systems for fluoride levels is recommended in order to safeguard the consumer’s health.