Based on a total of 135 stable isotope analysis (δ18O, δD) carried out on surface and groundwater samples, as well as on rainwater samples between 2004 and 2011 in 5 different regions in Baja California, an isotopic evaluation of the region was established. The results showed a depletion gradient of -0.25 ‰ δ18O per 100 m rise in elevation throughout the study area. Considering an unaltered δ18O signature for the thermal springs, the recharge areas of these waters are at elevations over 1400 m outside of the present watersheds, indicating the presence of regional flow systems next to the local flow regime feeding the cold springs and wells. The Mesa de Andrade area has a completely different signature with values of -105 for δ18O and -13 for δD.