Thermal water samples from Yellowstone National Park (YNP) have a wide range of pH (1–10), temperature, and high concentrations of fluoride (up to 50 mg/l). High fluoride concentrations are found in waters with field pH higher than 6 (except those in Crater Hills) and temperatures higher than 50 °C based on data from more than 750 water samples covering most thermal areas in YNP from 1975 to 2008. In this study, more than 140 water samples from YNP collected in 2006–2009 were analyzed for free-fluoride activity by ion-selective electrode (ISE) method as an independent check on the reliability of fluoride speciation calculations. The free to total fluoride concentration ratio ranged from <1% at low pH values to >99% at high pH. The wide range in fluoride activity can be explained by strong complexing with H⁺ and Al³⁺ under acidic conditions and lack of complexing under basic conditions. Differences between the free-fluoride activities calculated with the WATEQ4F code and those measured by ISE were within 0.3–30% for more than 90% of samples at or above 10⁻⁶ molar, providing corroboration for chemical speciation models for a wide range of pH and chemistry of YNP thermal waters. Calculated speciation results show that free fluoride, F⁻, and major complexes (HF(aq)0, AlF²⁺, AlF2+and AlF30) account for more than 95% of total fluoride. Occasionally, some complex species like AlF4-, FeF²⁺, FeF2+, MgF⁺ and BF2(OH)2- may comprise 1–10% when the concentrations of the appropriate components are high. According to the simulation results by PHREEQC and calculated results, the ratio of main fluoride species to total fluoride varies as a function of pH and the concentrations and ratios of F and Al.