The reason to put it in the drinking water is to get the fluoride incorporated into the baby teeth, but more importantly, into the permanent teeth, while they are developing. Applying fluoride to the outside of the teeth at the dentist's office, or with tooth-paste, seems to be less effective than if the fluoride is distributed through-out the tooth.

"The prevalence of dental caries in a population is not inversely related to the concentration of fluoride in enamel, and a higher concentration of enamel fluoride is not necessarily more efficacious in preventing dental caries... The laboratory and epidemiologic research that has led to the better understanding of how fluoride prevents dental caries indicates that fluoride's predominant effect is posteruptive and topical and that the effect depends on fluoride being in the right amount in the right place at the right time. Fluoride works primarily after teeth have erupted, especially when small amounts are maintained constantly in the mouth, specifically in dental plaque and saliva. Thus, adults also benefit from fluoride, rather than only children, as was previously assumed."