Water resources management has a crucial role not only for assuring human consumption but also for the structural development of the country, especially regarding power generation, industry and agriculture. Although water is an abundant resource in Brazil, the country currently faces a moment of hydro insecurity, with risks of shortage in the southeast and northeast, exposing management flaws. In this context, groundwater becomes a strategic reserve. Discussing the protection of aquifers becomes crucial to ensure water security, once groundwater has an enormous potential to provide water supply in adequate quality and quantities for human use. Such resource can and should be used, but in a sustainable, rational and coordinated way, in order not to be compromised for present and future generations. The Brazilian Constitution entrusts the State Government with managing groundwater. Each State determines their own management rules whether in the State Water Policies, or in environmental laws and regulations specifically addressed to this issue. These rules, in general, bring appropriate tools for the protection of this resource. However, in practice, they are not always applied in an effectively way, what results in a real gulf between legal provision and the actual protection and management of groundwater. Such issue becomes even more complex, considering that the boundaries of the aquifers do not follow political boundaries of states, nor the watershed boundaries. Major aquifers are shared by several states. As an example, the Guarani Aquifer System (GAS), the biggest in the world, covers 8 states of the federation and 3 other countries besides Brazil, and the Urucuia Aquifer System (UAS) 6 states. Isolated policies over shared bodies of water are far from ideal, since the overall impact on the aquifer ends up not being considered, which may result in overexploitation or pollution. If on the one hand integrated actions seem to be the only way to manage these water bodies, on the other hand joint actions between these various states are an extremely challenging task. All this complexity is aggravated by the fact that this topic is fairly new and still little is known about the aquifers in Brazil. Effective management of these resources requires accurate knowledge of their availability, their uses, and the existing demands. Therefore, to improve groundwater management, a key step is to identify, in practice, what are the main challenges faced by state entities for its protection. In order to guide actions to protect and correctly use groundwater in Brazil, we highlight the need for institutional coordination between agencies and state entities in the application of the instruments provided in public water policies, especially related to Water Resources Plans, information systems and the granting of rights to use water. The application of these instruments must be made in an articulated way between states that share the same aquifer, with a systematic exchange of information, so that the use of these resources can be equitable, allowing everyone access to groundwater. In addition to the above-mentioned instruments of water management, it is important to emphasize the possibility of the creation of Conservation Units in areas of upwelling or groundwater recharge, as a way of limiting the use of the soil and prevent contamination from these pathways. Although under Brazilian Constitution groundwater resources belong to State Government, as mentioned above, the role of the Municipalities must also be taken into account in the protection of groundwater, once the Municipalities are in charge of land use control. Along this line, there must be a strong link between States and their Municipalities in the aquifers incidence areas, in order to establish ways of joint land use and management. In this manner, the application of economic instruments in the search for effective protection of aquifers must be considered, such as legal provisions regarding access to state funding and other types of incentives, specifically for municipalities to consider groundwater and their fragility in their land use policies, and effectively comply with the rules laid down for groundwater protection. 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