The Tibetan Plateau (TP) is known as the “Asian Water Tower” and provides vital drinking water for residents of China and Southeast Asian countries. However, large-scale regional research on water quality in this climate-sensitive and eco-fragile area is still lacking. Considering that drinking from fluoride-contaminated water has posed serious health concerns worldwide, especially in Asian counties, it is urgent to clarify the spatial-temporal distribution characteristics, influencing factors, and health risk of fluoride in surface water in the TP. In this study, a total of 2697 surface water samples from major rivers and typical lakes in the TP were systematically analysed. Overall, fluoride concentrations ranged from 0.005 mg L−1 to 6.240 mg L−1 and varied among water periods, water basins and even water types. Pearson’s correlation analysis showed that the distribution of fluoride concentration was closely related to regional climate and positively correlated with anthropogenic activities. Probabilistic health risk assessment revealed that potential hazards in the Inner basin remained highest for all age groups (HR>1), especially for infants and adults (HR>3), while the risks in most other water basins were acceptable (HR < 1). In addition, more than 75% of the residents affected by the surface water in the TP were assessed as having a low fluoride exposure health risk. Our findings can provide scientific support for fluorosis prevention, as well as guide water resource utilization in the TP and adjacent region.