AbstractThis paper presents an approach to estimate the effects of a managed recharge experiment in a multilayer aquifer characterized by the presence of perched water tables in the Medina del Campo groundwater body, Douro basin, central Spain. A numerical model was developed to evaluate the effect of artificial recharge on the shallow sector of a regional‐scale aquifer and on formerly active wetlands. The model was developed in the Visual MODFLOW Pro v.2011.1 environment in order to represent and analyse the regional impact of this artificial recharge event. Results suggest that the assumption of a single perched system may prove useful in regional contexts where data is limited. From a study site perspective, managed recharge is observed to increase shallow storage along the riverbanks, which is considered valuable for environmental purposes. However, downstream wetlands are unlikely to experience a significant recovery. Furthermore, only a small percentage of artificial recharge is expected to reach the deep regional aquifer. This method can be exported to settings characterized by the presence of perched aquifers and associated groundwater dependent ecosystems.