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Water supply in semiarid areas in Mexico depends on water extraction from compartmentalized aquifers where large drawdown rates can be observed due to increasing demand from urban, industrial and agricultural users. Understanding the behavior of these aquifers is a necessity in order to improve the estimation of water balances. Accordingly, this study assembles both geochemical and isotopic data to identify the source of recharge to the San Juan del Río graben aquifer and to determine its dynamics. The geological model developed with the aforementioned data reveals a complex system composed of a heterogeneous multilayered compartmentalized aquifer. The San Juan del Rio basin is composed of (1) the Amealco perched aquifer, (2) a shallow granular aquifer, and (3) a fractured aquifer. Hydrogeochemical and isotopic data (δ2H, δ18O, δ13C and correct carbon activity (Δ14C)) allow for identification of three end-member sources: (1) local meteoric recharge, (2) old groundwater contained in the siliciclastic shallow aquifer, and (3) regional/local hydrothermal recharge. The contribution of both meteoric and regional hydrogeothermal flow to the different aquifer compartments is determined through a principal component analysis of the hydrogeochemical data. With the aforementioned analysis it was found that the dominant contribution source for all aquifer compartments is meteoric water (up to 60% with a median of 50%), while the regional hydrothermal groundwater contribution represents 15%, even for the shallow aquifer. [ABSTRACT FROM AUTHOR]