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The Katari River Basin, a key watershed feeding Lake Titicaca, is severely contaminated due to mining waste, urban effluents, industrial discharges, and agricultural runoff. These pressures have disproportionately affected downstream Indigenous Aymara communities, threatening their rights to clean water, food security, and cultural continuity. This study examines citizen science as a participatory approach through which Indigenous communities engage with environmental justice concerns in their territories. Through a participatory process involving local community members, 46 water samples were collected over a four-month period and analysed using low-cost monitoring methods. Results show consistent exceedances of Bolivia's national water quality standards, particularly for total dissolved solids, phosphate, and turbidity, with the most severe breaches occurring in the Katari River. Findings were presented and discussed during community workshops on Indigenous and environmental rights, facilitating collective interpretation and dialogue. These workshops were complemented by 20 semi-structured interviews exploring how participants responded to the scientific evidence in relation to their lived experiences. A thematic analysis reveals that citizen science can foster environmental knowledge, intergenerational dialogue, and awareness of environmental rights and responsibilities, while remaining insufficient on its own to generate distributive or institutional environmental justice outcomes in the absence of legal literacy, institutional responsiveness, and formal accountability mechanisms. Drawing on a resources nexus lens, the findings also highlight the interdependence of water quality, food systems, and cultural integrity, emphasising the need for rights-based, community-anchored approaches to environmental governance in Indigenous contexts.