The objective of this study was to evaluate the association between in utero exposure to fluoride (F) and Mental and Psychomotor Development (MDI and PDI) evaluated through the Bayley Scale of Infant Development II (BSDI-II) in infants. The sample included 65 mother-infant pairs. Environmental exposure to F was quantified in tap and bottled water samples and F in maternal urine was the biological exposure indicator; samples were collected during the 1st, 2nd and 3rd trimester of pregnancy. The mean values of F in tap water for the 1st, 2nd and 3rd trimester were 2.6 ± 1.1 mg/l, 3.1 ± 1.1 mg/l and 3.7 ± 1.0 mg/l respectively; above to 80% of the samples exceeded the reference value of 1.5 mg/l (NOM-127-SSA1-1994). Regarding F in maternal urine, mean values were 1.9 ± 1.0 mg/l, 2.0 ± 1.1 mg/l and 2.7 ± 1.1 mg/l for the 1st, 2nd and 3rd trimester respectively. The infants with MDI and PDI scores less than 85 points were 38.5% and 20.9% respectively. After adjusting for potential confounding factors (gestational age, age of child, marginalization index and type of water for consumption), the MDI showed an inverse association with F levels in maternal urine for the first (β = −19.05, p = 0.04) and second trimester (β = −19.34, p = 0.01). Our data suggests that cognitive alterations in children born from exposed mothers to F could start in early prenatal stages of life.