Chilika Lagoon, Asia’s largest brackish water ecosystem, is shaped by the complex interactions between ecological processes, local livelihoods, and governance frameworks. However, challenges such as climate change, pollution, and unsustainable practices are degrading biodiversity and water quality, threatening the viability of small-scale fisheries (SSFs). This study examines how blue carbon ecosystems (BCEs), water quality, and adaptive governance contribute to the resilience of SSF communities. Using qualitative methods—including interviews, participant observation, and thematic analysis—we analyze the adaptive strategies of fishers, the role of community engagement, and governance mechanisms in sustaining SSFs. Our findings emphasize the importance of participatory decision-making, localized knowledge, and flexible governance structures in enhancing resilience. By integrating ecological, social, and institutional perspectives, this research contributes to broader discussions on sustainable fisheries and the governance of food systems in the Global South. The study offers valuable insights for policy interventions that support both environmental sustainability and the well-being of SSF communities.