Background: Fluoridation of public water systems is known as a safe and effective strategy for preventing dental caries based on evidence from non-randomized studies. Yet 110 million Americans do not have access to a fluoridated public water system and many others do not drink tap water. This article describes the study protocol for the first randomized controlled trial (RCT) of fluoridated water that assesses its potential dental caries preventive efficacy when delivered in bottles., Methods: waterBEST is a phase 2b proof-of-concept, randomized, quadruple-masked, placebo controlled, parallel group, trial designed to estimate the potential efficacy of fluoridated versus non-fluoridated bottled water to prevent dental caries incidence in the first four years of life. Two hundred children living in eastern North Carolina, USA, and aged 2-6 months at screening are being allocated at random in a 1:1 ratio to receive fluoridated (0.7 mg/L F) or non-fluoridated bottled water sourced from two local public water systems. Throughout the 3.5-year intervention, study water is delivered monthly in 5-gallon bottles to each child's home with instructions to use it whenever the child consumes water as a beverage or in food preparation. Parents are interviewed quarterly to monitor children's water consumption and health. At annual visits, the presence of dental caries is evaluated with a dental screening examination. Clippings from fingernails and toenails are collected to quantify fluoride content as a biomarker of total fluoride intake. The primary endpoint is the number of primary tooth surfaces decayed, missing, or filled due to dental caries measured by the study dentist near the time of the child's fourth birthday. Tooth decay is assessed at the threshold of macroscopic enamel loss. For the primary aim, a least-squares, generalized linear model will estimate efficacy and its one-tailed, upper 80% confidence limit., Discussion: waterBEST is the first evaluation of a randomized intervention of fluoridated drinking water in bottles to prevent dental caries in the primary dentition. This innovative method of delivering fluoridated water has potential to prevent early childhood caries in a large segment of the U.S. population that currently does not benefit from fluoridated public water., Competing Interests: Competing interests {28} The authors declare they have no competing interests.