This article discusses the issue of water quality restoration in Guanabara Bay, a much polluted estuary, located in Rio de Janeiro, Brazil, which serves as drainage basin for 11 million people. The theoretical basis for analyzing the problem is the systems approach, and the focus is on devising actions to achieve the modernization of the sanitation sector. In order to restore the bay’s water quality, specific targets measured in terms of the level of biochemical oxygen demand (BOD) need to be attained. The Guanabara Bay system contains five components: decision support tools, physical infrastructure, financing, governance, and administration. The article proposes a policy approach that seeks to attend to the environmental concerns associated with the restoration of the bay’s water quality by advocating an effective governance structure able to provide sanitary services to all citizens that will also mitigate the bay’s pollution problems.