River infrastructure, such as dams, weirs, and channel alterations, greatly affects global fish biodiversity by disrupting habitat connectivity, water flow patterns, and the overall ecological balance. Current development of hydropower in Indonesia, as one of river infrastructures, is potentially affecting the connectivity of river systems, disrupting the natural migration patterns of fish, particularly juvenile anguillid eels, and leading to population declines. Additionally, the lack of information on juvenile eel migration in Indonesian rivers hinders the understanding of their population dynamics. This study aims to assess the population dynamics of upstream-migrating juvenile eels and explore strategies to enhance their migration in a hydropower-regulated tropical river. The research will investigate the population and biochemical characteristics of juvenile anguillid eels in hydropower-regulated river in Indonesia. Additionally, this study will evaluate the climbing performance and physiological parameters of juvenile anguillid eels on different substrate types, providing insights into their migratory behaviour and the physiological responses that influence their success in overcoming barriers created by hydropower infrastructure. The findings will contribute to the development of sustainable management practices for eel fisheries, highlighting the need for effective strategies to improve juvenile eel passage and ensure the long-term viability of eel populations in fragmented habitats. Ultimately, this study seeks to inform policymakers and conservationists about the importance of integrating ecological considerations into hydropower planning and management to promote a balance between energy production and the preservation of aquatic biodiversity.