Most of Brazil’s natural waters are stored in aquifers, with great potential for meeting supply demands. A comprehensive environmental management is, thus, fundamental for preserving this resource and preventing threats to human health and to the environment. Nonetheless, practices are heterogenous throughout the country; the legislation in the wealthiest state, Sao Paulo, has been historically a reference at a federal level. The database from the environmental agency of the state of Sao Paulo was analysed, particularly the cases of contaminated sites by chlorinated solvents. Not only these are a major industrial contaminant, but contaminated industrial sites are notably underestimated in the state registry. An in-depth analysis revealed a challenging scenario in which many private supply wells are within or neighbouring potentially or known contaminated areas. Additionally, despite the common environmental and contamination complexities, the pace of rehabilitation in industrial sites surpasses the average discovery of new contaminated sites, bringing attention to efficiency and the accuracy of the remediation methods applied. Finally, the need to advance the approach when dealing with complex industrial contaminated sites in Brazil is discussed. The key challenges highlighted in this work include complex and heterogeneous nature of subsurface environments, gaps in existing legislation to present a framework for groundwater monitoring and management, and limitations of government structure.