The intensive use of the Aquifer of the Metropolitan Zone of Mexico City (AMZMC) has increased the concentrations of some trace elements due to natural or anthropogenic sources, as the release of elements from the heterogeneous mixture of the volcanic rocks and/or alluvial clay deposits, which play a very important hydrogeological role in the behavior of the aquifer. This study characterizes, examines, and compares the concentrations of Ba, B, Sr, and Rb in some wells of the AMZMC. Characterization of major elements and Ba, B, Sr concentration and their behavior in the aquifer, and some ionic ratios have been used to identify the dominant hydrogeochemical processes and the different sources of Rb, Ba, B, Sr in the water, in which mineral alteration, ion exchange, redox reactions are the dominant processes, and may intensify as the salinity, temperature and ionic strength in the medium increases. This information may be indirectly relevant as a contribution to the development of appropriate water management strategies in Mexico City. In addition to providing new data on the distribution and behavior of Rb, Ba, B, Sr in groundwater of the Mexico City Aquifer, which is used for drinking water supply. •The aquifer located in a fractured volcanic environment has natural Ba, B, Sr and Rb high contents.•Ba, B, Sr and Rb mobilization is consequence to hydrogeochemical reactions such as ion exchange, silicate weathering, carbonate dissolution and redox reactions that take place at depth.•The cationic exchange affects Ca and Sr concentrations, when increase the salinity and ionic strength by an increase in Cl-.•The behavior of Ba, Sr, B, Rb and K can decrease and increase due to redox conditions and pH in the aquifer.