Severe shortage in good quality water reserves is a global problem that will increase with a growing world population. Managed Aquifer Recharge (MAR) will contribute to replenish depleted aquifers and restore ecological services in fresh water ecosystems. However, risks associated to the occurrence of pathogens and anthropogenic emerging pollutants in groundwater have led to question the reuse of reclaimed water for MAR. MARadentro aims to assess and minimize these risks, and to increase the benefits of MAR guaranteeing human health and environment protection through the development of affordable and effective permeable reactive layers. These integrate biotic and abiotic processes to enhance pathogen retention and inactivation and pollutant adsorption and degradation by making available a broad range of sorption sites and a sequence of redox states. The applicability of the proposed MAR layers will be validated by upscaling from lab and pilot experiments to field scale studies. Transport modelling, risk assessment, economic balance and establishment of recommendations to stakeholders and authorities in the water sector will guarantee the smooth implementation of this MAR concept and the positive public response to water reuse. The transfer of the knowledge gathered in MARadentro to policy makers will help in EU regulation on MAR.