Citizen science is a widely used tool in research and project management. In a well-grounded field based initiative in the Mahakali basin, this is being contextualised, applied, and tested as a framework to address the various challenges associated with transboundary water governance. Some of the challenges are primarily caused by a lack of coordination between administrative and governance systems and communities in Nepal and India, mutual accusations regarding emerging water risks and vulnerabilities, and limited information about quality of river water. This paper is based on grassroots work by the authors that aimed at addressing the existing gaps in community-led water governance and to strengthen transboundary water governance systems, in the Mahakali basin involving communities from both India and Nepal. The framework consists of building capacities of communities on various components of science and local practices and fostering dialogue among communities to encourage local actions for improving water quality. This citizen science has evolved to be a promising method for strengthening dialogue among local communities, local government, and civil society organisations, further increasing the scope of transboundary water co-operation in the Mahakali basin. The work has helped bring about a clear shift in the narrative and discourse from ‘water sharing’ to ‘water conservation’, creating a positive environment for future dialogues and commitment to joint action. This paper, emphasises mainstreaming citizen science in transboundary water governance systems, fostering awareness and solidarity among riparian communities. It also argues that citizen science can be an excellent tool for leveraging culture and local systems to improve water quality and promote cultural harmony in transboundary regions. Besides, it carries the potential to create and deepen the needed systems that help ensure environmental and cultural sustainability in regions with shared resources.