Endemic arsenic poisoning and fluorosis caused by primary high arsenic (As) and high fluoride (F−) groundwater have become one of the most serious environmental geological problems faced by the international society. High As and high F− groundwater exists in Neogene confined aquifers in Guide basin, with concentrations of 355 μg/L and 5.67 mg/L, respectively, and showing a co-occurrence phenomenon of As and F− in the groundwater. This poses a double threat to the health of tens of thousands of local residents. In this study, based on the systematic collection of groundwater and borehole sediment samples, analysis of hydrochemistry and isotope indexes, combined with laboratory tests, purpose of this study is to reveal the migration rule and co-enrichment mechanism of As and F− in aquifers, and finally establish a hydrogeochemical conceptual model of the enrichment process of As and F−. The main conclusions are as follows: hydrochemical type of unconfined and confined groundwater in Guide basin is Ca–Na–HCO3 and Na–Cl–HCO3 type, respectively. Main minerals in sediments are quartz and plagioclase. Concentrations of As and F− are lower in unconfined groundwater, but higher in confined groundwater, and which show a gradual increasing trend along the groundwater flow path. The mineralization of natural organic matter in confined aquifer causes iron and manganese oxide minerals containing As to dissolve gradually, which leads to the gradual release of As into groundwater. Large amount of HCO3− produced by mineralization of organic matter precipitate with Ca2+ in groundwater, resulting in reduction of Ca2+ content, promoting the dissolution of fluoride-containing minerals such as fluorite (CaF2), and continuously releasing F− into groundwater. Meanwhile, competitive adsorption reactions in confined aquifers causes more As and F− to be released from mineral surface into groundwater, which gradually migrate and accumulate along groundwater flow. Finally, it is established that a conceptual model for the formation of high As and F− groundwater in the confined aquifer of Guide basin. The research results not only help to improve our understanding of the formation and evolution of groundwater with high As and F− with similar geological background, but also provide scientific basis for rational development and utilization of groundwater, and prevention and control of chronic As and F− poisoning in local and similar areas.