The San Juan Estuary Bay is place of many contrasts. On one hand, is one of the most valuable ecosystems within Puerto Rico’s Metropolitan Area. On the other, the urbanization of nature through the Island modernization process has resulted in historic water quality problems. Recently, the SJEBP identified 12 critical areas where there are serious water contamination problems due to sewage discharges. The challenge now consists in generating the public participation and environmental policy action framework to foster its restauration on the long run. In this article we reflect upon the possibilities of community-based water quality monitoring as an approach to cultivate a political consciousness and environmental activism about water relations in the city. Through the lenses of Political Ecology, Participatory Action Research and Popular Education we reflect upon some preliminary findings about a current research effort aimed at documenting the water conflicts and generate the social mobilization needed to contribute to SJEB restauration.