Reversing the chemical and quantitative impacts derived from human activity on aquifers demands a multidisciplinary approach. This requires, firstly, to update the hydrogeological knowledge of the groundwater systems, which is pivotal for the sustainable use of this resource, and secondly, to integrate the social, economic and administrative reality of the region. The present work focuses on the Benalup aquifer, whose exploitation plays a major role in the economy of the area, based mainly on irrigated agriculture. This activity has had negative consequences for the aquifer in quantitative and chemical terms, leading to its declaration as in poor condition. The study presented here shows the results obtained from the application of hydrogeological techniques, remote sensing and citizen participation tools, which have allowed us to deepen and improve the current knowledge of the system’s hydrogeological, geometric, administrative and social aspects. Additionally, the lessons learned from this case study are analyzed. The deficiencies detected are discussed, and alternatives aimed at the sustainable use of groundwater are proposed, such as the possibility of a joint use of surface and groundwater resources, the creation of a Water User Association responsible for the management of groundwater and the need for greater efforts aimed at educating and raising awareness of water conservation among citizens.