The San Luis Potosí valley is an endorheic basin that contains three aquifers: a shallow unconfined aquifer of alluvial material and two deep aquifers, free and confined. The groundwater contamination documented for the shallow aquifer generates contamination of the deep unconfined type aquifer, from which part of the population’s drinking water needs are met. This study records incipient anthropogenic contamination of two types: biogenic and potentially toxic trace elements. The studied contaminants include fecal coliform bacteria, total coliform, nitrate, and potentially toxic elements such as: manganese (Mn), mercury (Hg), arsenic (As), and cadmium (Cd). This contamination in some locations exceeds the permissible limit for human consumption. Some major consequences to health, including severe illness, may be caused by the trace elements. The present results give a first signal about the contamination of the deep unconfined type aquifer due to anthropogenic activity in the valley. This is a priority issue because this aquifer supplies drinking water, and in the short or medium term it will have an effect on public health.