The concept of a “water governance crisis” manifests distinctly across different regions. In the Global South, particularly in rapidly urbanizing cities, innovative governance models that incorporate community participation are critically needed to address unique challenges such as informal settlements and less stringent pollution controls. This paper presents a theoretical and methodological approach, emphasizing citizen science and community engagement in urban water management. It explores how engaging communities in the assessment and management of water bodies not only enhances the identification of priority areas but also strengthens local capacities to address environmental challenges. An analytical framework highlighting the interdependence between valuation languages and citizen science supports the development of management models for degraded hydro-social territories. Utilizing a mixed-methods approach, this research develops social indicators and applies participatory methodologies, such as Participatory Mapping, demonstrated through a study of four urban rivers in Sangolquí, Ecuador: Santa Clara, San Pedro, Pita, and San Nicolás. Our findings reveal that participatory models are more effective than traditional technocratic hierarchies and underscore a new paradigm for water governance that prioritizes local knowledge and community practices. This study not only reveals the ecological, social, and spatial configurations of urban river landscapes in Sangolquí but also suggests the framework’s applicability to other Latin American cities facing similar challenges.