A groundwater sampling campaign was carried out in the summer of 2013 in a low-temperature geothermal system located in Juventino Rosas (JR) municipality, Guanajuato State, Mexico. This groundwater presents high concentrations of As and F⁻ and high Rn counts, mainly in wells with relatively higher temperature. The chemistry of major elements was interpreted with different methods, like Piper and D’Amore diagrams. These diagrams allowed for classification of four groundwater types located in three hydrogeological environments. The aquifers are hosted mainly in alluvial-lacustrine sediments and volcanic rocks in interaction with fault and fracture systems. The subsidence, faults and fractures observed in the study area can act as preferential channels for recharge and also for the transport of deep fluids to the surface, especially in the basin plain. The formation of a piezometric dome and the observed hydrochemical behavior of groundwater suggest a possible origin of the As and F⁻. Geochemical processes occurring during water–rock interaction are related to high concentrations of As and F⁻. High temperatures and alteration processes (like rock weathering) induce dissolution of As and F⁻-bearing minerals, increasing the content of these elements in groundwater.