<p>This study evaluates the ecological health and governance challenges of Nagi and Nakti Ramsar sites in Bihar, India, recently designated Ramsar Sites, to inform a framework for sustainable conservation. Seasonal assessments of water and soil quality revealed significant physicochemical fluctuations, particularly during the dry season, marked by reduced depth, increased mineralization, and nutrient accumulation. Two-way ANOVA indicated that water parameters such as pH, temperature, dissolved oxygen, total alkalinity, and Secchi depth varied significantly across seasons, sanctuary type, and their interaction. Soil organic carbon and phosphorus also showed seasonal shifts, influencing nutrient cycling and habitat fertility. Plankton dynamics were strongly linked to phosphorus levels, supporting the growth of Bacillariophyceae and Chlorophyceae. Zooplankton composition differed between sites, with rotifers dominant in Nagi and cladocerans in Nakti. Thirty fish species were documented, mainly omnivores and insectivores, with Cyprinidae as the most abundant family. While the presence of diverse biota reflects ecological richness, emerging stressors such as nutrient loading and invasive species are evident. Notably, tilapia stocking poses a serious threat to native small indigenous fishes (SIFs) through competition and habitat disruption. Governance analysis revealed overlapping jurisdictional control between the Forest and Irrigation Departments, weak community involvement, and inadequate regulation of tourism activities. To address these issues, a polycentric, participatory governance model is proposed, integrating ecological monitoring, local livelihoods, and conflict resolution. The study highlights the urgency of adaptive, inclusive management to balance biodiversity conservation with socio-economic sustainability, offering a replicable model for freshwater protected areas in South Asia.</p> Graphical abstract <p></p>