In Northern Baja California environmental conservation may not be fully accomplished in the absence of a clear understanding of key factors controlling and protecting biodiversity Groundwater is an environmental agent triggering the presence of a wide range of arid ecosystems therefore any sustainable development in the region has to maintain a balance between environmental social and economical benefits The present study has placed a great emphasis on the understanding and distribution of groundwater flow systems and their environmental interactions in the protected area of the Valle de Los C iacute rios using physical chemical and isotope methods Results show the presence of three groundwater groups portraying contrasting flow systems conditions Analyzed samples have been classified as fresh brackish and thermal alkaline groundwater as suggested by pH temperature and TDS The Br Cl ratio in most samples was close to the ocean molar value x indicating the importance of marine aerosol fraction in the recharged waters however Mg Cl Na Cl Ca Cl SO Cl and Cl HCO Cl ratios were significantly different to those of seawater mixing conditions Dominant ions Na Ca and Cl chemical age proxies Li and O suggest waters with long residence time with the possibility of been recharge during the late glacial period Thermal ground water shows low minor and trace element content and exhibits the dominance of Na plagioclase hydrolysis their low levels of Sr and Ba suggest negligible contact with calcareous rocks and their estimated temperature at depth to deg C and TDS suggest groundwater has travelled through fractured media This introduction study suggests that desertic species in Valle de Los Cirios are highly sustained by groundwater of local and intermediate flows