This article discusses how new contributions from hydrogeological science in the 20th and 21st centuries have allowed for a better understanding of the processes that affect the maintenance of river flows. Moreover, the way in which this knowledge has been conveyed beyond academia and has been gradually incorporated into public policy for natural resource management is also discussed. This article explains the development of several approaches used to understand the relationships among the management of aquifers, vegetation and river flows, including water balance, aquifer recharge, the piston effect, seasonal effects, and safe and sustainable yields. Additionally, the current challenges regarding the modeling of hydrological processes that integrate groundwater and surface waters are discussed. Examples of studies applied in Brazil that demonstrate these processes and stimulate thought regarding water management strategies are presented. In light of the case studies, it is possible to propose different strategies, each adapted for specific hydrogeological context to maximize aquifer recharge or base flow maintenance. Based on these strategies, the role of infiltration ponds and other artificial recharge techniques is re-evaluated in the context of the mitigation of environmental impacts on the maintenance of river flows. Proposals for the improvement of public policies regarding the payment of related environmental services to stimulate investment in aquifer recharge and the maintenance of base flow, for which the goal is to attain win-win-win situations for the environment, farmers and water users, while preventing land speculation, are discussed. Lastly, a conceptual model for the dissemination of hydrogeological knowledge in public policies is provided, and its challenges and possibilities are discussed.