Fluoride is an essential trace element for humans, and its deficiency or excess in the environment could lead to disease. To investigate the spatial distribution and health risk assessment of fluoride (F⁻) in drinking water, 302 tap water samples from Chongqing urban areas, China, were collected to analyze F⁻ using an ion chromatograph. The results showed that (1) F⁻ concentration in drinking water ranged from 0.100 to 0.503 mg/L, with an average of 0.238 ± 0.045 mg/L. (2) The spatial autocorrelation analysis showed that high–low clusters were mostly located in Dadukou District and Beibei District, while low–low clusters were mainly in southern Banan District. (3) The fluoride average daily doses of children, teens and adults were 0.030, 0.029 and 0.031 mg/(kg day). (4) Hazard quotients of excessive fluoride (HQ_e) of children, teens and adults were 0.51 ± 09, 0.49 ± 0.09 and 0.52 ± 0.10, respectively (inferior to 1.00), whereas hazard quotients of inadequate fluoride (HQ_i) of those groups were 1.21 ± 0.26, 1.23 ± 0.26 and 1.15 ± 0.25, respectively (superior to 1.00). Therefore, average daily fluoride intake of residents with drinking water was inadequate. This could pose dental caries and osteoporosis threats for residents from Chongqing urban areas.