In arid and semiarid regions, groundwater becomes the main source to meet the drinking water needs of large cities, food production, and industrial activities. For this reason, necessary studies must be carried out to estimate its quantity and quality, always seeking sustainable management, thus avoiding social conflicts or a decrease in the productive activities of humanity. This research explains the behavior of groundwater quality concerning arsenic speciation and its relationship with fluoride. The average total arsenic concentration of 19.95 µg/L and 20.29 µg/L is reported for the study period from 2015 to 2020, respectively, according to the Mexican standard. If the population drinks water directly, it is exposed to possible damage to health. The predominant arsenic species is As (V), with 95% and As (III) with 5%, this finding will allow us to define in greater detail the type of remediation that is required to reduce the content of this element in the water. Regarding the relationship between arsenic and fluorine, very small Pearson correlation coefficients of the order of 0.3241 and 0.3186 were found. The estimation of the space–time variation made it possible to identify the areas with the highest concentration of arsenic and fluorine, allowing the definition of the operating policies of these wells, thereby protecting the health of the inhabitants who consume this water.