To determine the spatiotemporal distributions of fluoride and arsenic in the rivers within the mining districts of Kyrgyzstan and health risks associated with the use of these rivers, a total of 169 water samples were collected from the main rivers and tributaries of Kyrgyzstan from 2016 to 2018. Through the cold and hot spot analysis, multivariate statistical analysis and health risk assessment model, the results indicated that the fluoride and arsenic concentrations in river waters increased year by year from 2016 to 2018. According to the World Health Organization (WHO) drinking water guidelines, 0%, 1.09% and 1.06% of the analyzed samples exceeded the limit for fluoride (1.5 mg/L), and 0%, 1.09% and 2.13% of the samples exceeded the limit for arsenic (10 µg/L) in 2016, 2017 and 2018, respectively. The gathering areas for high fluoride concentrations were mainly distributed in the Issyk-Kul Basin, Chu River Valley and Fergana Basin, while high arsenic concentrations were mainly observed in the Chu River Valley and southern Fergana Basin. Although fluoride and arsenic were not found to exceed the limits simultaneously, the two pollutants accumulated high values in the southern Fergana Basin in 2018, which indicated the risk of joint poisoning. From 2016 to 2018, arsenic concentrations in the river water of Kyrgyzstan created a high risk of carcinogenesis by the ingestion intake exposure route, which resulted in the total risk of health hazards to children and adults caused by fluoride and arsenic to exceed the maximum acceptable ranges. Therefore, the national environmental protection department in Kyrgyzstan should strengthen the dynamic monitoring of arsenic concentration in the rivers, and related scientific research institutions should conduct more in-depth research on the migration and transformation process of pollutants, the toxic mechanism, and even the substantive countermeasures in the future.