Groundwater is an essential resource for society and the environment in Brazil. More than 557 m3/s (17.5 km3/y) are extracted through 2.5 million wells to meet demand in cities and the countryside, generating an economy of R$ 56 billion per year (US$ 14 billion/year). The aquifer has a remarkable function in the hydrological cycle because its large storage regulates the perenniality of rivers, lakes and preserves mangroves, marshes, and vegetation in dry periods. Aquifer discharges maintain between 24% (annual average) and 49% (dry season) of the flow of these surface water bodies. Although studies on groundwater quality are still restricted, it is known that most aquifers still preserve their excellent natural quality. Nevertheless, over the past years, there has been a growing increase in cases of contamination associated with: (i) natural geochemical anomalies (iron, manganese, and fluorine, secondarily, chromium, and barium, and rarely arsenic) due to the dissolution of specific minerals; and (ii) human contaminant activities, related to urban areas without sewage network, or with industrial activities, storage of hazardous products, and solid waste facilities. Among the anthropic compounds commonly handled, the most problematic are the chlorinated organic solvents and heavy metals, and in non-sewage areas, nitrate. The precarious knowledge of aquifer-quality, especially in cities, demonstrates the need to invest in regular and systematic hydrogeological research and mapping projects that drive to the improvement of the practices on aquifer quality protection.