Abstract. Managed Aquifer Recharge (MAR) is a worldwide used technique to increase the availability of water resources.We study how MAR modifies microbial ecosystems, and its implications for enhancing biodegradation processes to eventually improve groundwater quality. We compare soil and groundwater samples taken from a MAR facility located in NE Spain during recharge (with the facility operating continuously for several months) and after four months of no recharge. The study demonstrates a strong correlation between soil and water microbial prints with respect to sampling location along the mapped 5 infiltration path. In particular, managed recharge practices disrupt groundwater ecosystems by modifying diversity indices and the composition of microbial communities, indicating that infiltration favors the growth of certain populations. Analysis of the genetic profiles showed the presence of nine different bacterial phyla in the facility, revealing high biological diversity at the highest taxonomic range. In fact, the microbial population patterns under recharge conditions agree with the Intermediate Disturbance Hypothesis. Moreover, DNA sequence analysis of excised DGGE band patterns revealed the existence of indicator 10 species linked to MAR, most notably Dehalogenimonas sp, Nitrospira sp and Vogesella sp. Our real facility multidisciplinary study (hydrological, geochemical and microbial), involving soil and groundwater samples, support that MAR is a naturallybased, passive, and efficient technique with broad implications for the biodegradation of pollutants dissolved in water.