Over the past twenty years, there has been growing interest in the use of the subsurface for water storage using shallow ponds, where water is infiltrated to the subsurface and later groundwater is recovered from pumping wells. This scheme is designed as surface Managed Aquifer Recharge (MAR). Llobregat artificial recharge ponds are MAR systems located in alluvial aquifers near Barcelona with strong significance for water supply to the city. The recharge ponds showed low infiltration rates since the beginning (Ca n'Albareda) and a significant decrease after some months (Sant Vicenç). Consequently, different methodologies were designed for monitoring the systems and evaluating the effectiveness of the selected areas and maintenance procedures. For this purpose, we combined the use of Electrical Resistivity Tomography (ERT) with standard hydrogeological methodologies, including water table monitoring from piezometers and infiltration tests. The combination of direct and indirect methods have allowed us to improve the diagnosis of the subsurface involved in the managed recharge system. The ERT technique has shown to be a cost‐effective and high‐resolution tool, flexible and well adaptable for surveying at different scales without disturbing the recharge process. As a consequence, we demonstrate the usefulness of ERT imaging to unveil hydrogeological heterogeneities and monitoring infiltration, clogging effect and clean‐up processes in surface MAR projects.