The Basin of Mexico, where the Mexico City Metropolitan Zone (MCMZ) and its 20 million inhabitants are located, has had a two-sided approach towards water management, as it has struggled to drain the lakes that once covered this region while at the same time it started to transport in water from adjacent basins in the 1950s for water supply. In addition, the large amount of water extracted from the Basin’s aquifer have caused drawdown of the groundwater table and consequently, land subsidence which reaches 40 cm/yr in some areas. This work firts analyzes the existing water management policies in the Basin, and presents the development of a regional database called the Basin of Mexico Hydrogeological Database (BMHDB). This database was used to develop a daily soil water balance using different vegetation and soil types as well as the effect of topography on climatological variables and evapotranspiration used to estimate recharge to the Basin’s regional aquifer. Through the application of this model, it has been shown that the mountains that enclose the Basin of Mexico are the main recharge areas of the Basin’s regional aquifer.