Coastal Confluence Zones (CCZs), where rivers meet the sea, are ecologically rich and highly sensitive areas due to the unique mixing of freshwater and saltwater that supports a diverse array of plant and animal species. These estuarine environments are increasingly under pressure, particularly in Goa, where tourism-driven development and expanding fishing activities have intensified human dependency on ecosystem services. This study focuses on four riverine estuaries in South Goa—Sal, Saleri, Talpona, and Galgibag—to assess ecosystem service values and analyze livelihood dependencies, to enhance economic resilience while conserving critical ecological functions. Land use and land cover (LULC) analysis from 2003 to 2023 revealed significant transformations: a decline in forest, barren, and wasteland categories, alongside an increase in agricultural land. The study evaluated ecosystem services across four categories—provisioning, regulating, supporting, and cultural—quantified in economic terms (Rs/ha) to derive the Total Economic Value (TEV) of each CCZ. Among these, regulating services contributed the most to TEV in most CCZs, whereas cultural services had the least economic value. A literature-based assessment identified tourism and fishing as the two primary occupations linked to these ecosystems. Over the past decade, tourism-based livelihoods have become increasingly dominant across most CCZs, except in the Sal CCZ, where fisheries remain the primary source of income. Livelihood performance was analyzed across five capital assets—natural, physical, social, financial, and human—using a set of relevant indicators. The analysis showed relatively strong performance in terms of natural assets, but highlighted significant deficiencies in social, financial, and human capital in most CCZs. Based on these insights, the study proposes management guidelines aimed at fostering resilient estuarine ecosystems that support both ecological sustainability and socio-economic well-being. The findings underscore the importance of integrating ecosystem valuation with livelihood planning to achieve long-term economic resilience in Goa’s coastal confluence zones.