Riverine systems and associated fish populations worldwide are threatened by human impacts, especially in tropical countries with emerging economies. In India, community-based fish sanctuaries are a key mechanism for the conservation of freshwater fish populations, but there are few peer-reviewed studies on this subject. Here we integrate over 35 combined years of field experience with a literature synthesis to define and classify community-based fish sanctuaries. We present a novel, critical analysis of fish sanctuaries as social–ecological systems with a functional characterization based on natural capital, ecosystem services, human well-being, and policy and governance. We find that such sanctuaries are shaped by complex social–ecological processes, including coevolution of religious practices and ecological change, feedback processes created by retaliatory conflicts between river users, and diverse and dynamic governance strategies. These sanctuaries hold great potential for the conservation of rare fish species in India, but are subject to myriad threats at local, regional and global scales. Given the complexity of these social–ecological systems, we outline their conservation potential and highlight directions for future research.