Multidisciplinary information such as geophysical, hydraulic, geological, and hydrogeological information combined with GIS can be a powerful tool to better understand aquifers. The aim of this paper is to assess groundwater pollution risk through regional hydrogeological and local hydrogeophysical models built from multidisciplinary information and geophysical well logs. Once the regional model of the Toluca Valley Aquifer (Mexico) was built, the critical area (CA) of the aquifer was identified through features such as fractures and faults, pollution sources, subsidence, groundwater table depletion, and well density, which were transformed into GIS with multicriteria analysis. With the CA a local hydrogeophysical model was set to extract lithological information and compute the intrinsic vulnerability (IV) through the Dar Zarrouk parameters according to the AVI-Fr method which considers the influence of fractures and faults as preferential paths for pollutants. On the other hand, the potential harmful load (PHL) of the different pollution sources was estimated with the POSH method. Finally, with the relation between the IV and PHL, risk pollution map could be made. The results of this study show that different areas are exposed to pollution risk due to their proximity to fractures, oil and gas subsurface infrastructure and high pumping ratios and their relationships. The available geophysical data and multidisciplinary information were powerful tools for identifying the critical area of the TVA and proposing actions to mitigate or control excessive withdrawals for sustainable management.