<p>The global freshwater ecosystems are under tremendous pressure from challenges, including urbanisation, climate change, invasive species, and unsustainable resource use which are prominent in Eastern Himalayan region. The Northeast India has huge freshwater fish diversity; however, its fragile aquatic habitats face several biotic and abiotic threats which endanger the region’s ecological integrity and long-term sustainability. This study aims to assess the multiple ecological threats currently affecting the freshwater ecosystem and further examines the role of Traditional Ecological Knowledge (TEK), Indigenous Technical Knowledge (ITK), and Community-Based Fishery Management (CBFM) in fostering sustainable resource use. The study emphasises the significance of community-based fisheries management, which, when effectively integrated, is essential for grassroots development and local-level understanding of conservation. This integration can significantly enhance ecosystem resilience and support inclusive, sustainable livelihoods. Additionally, the paper explores the potential of Aqua-based Ecotourism as a conservation and economic strategy adding value to the conservation of endangered, threatened species requiring urgent attention. The research is based on a systematic review of existing literature, drawing on both regional and global case studies to provide comparative insights. Loktak Lake in Manipur, India which faces serious ecological deterioration due to anthropogenic and climatic pressures is the only floating lake and a designated Ramsar site has been considered as a case study to illustrate site-specific challenges in this work. With integration of TEK/ITK and scientific policy-driven approaches, this paper advocates for holistic, participatory conservation strategies and community engagement to safeguard the long-term sustainability of freshwater ecosystems in the Eastern Himalayas.</p>