South Korea’s River Act mandates the maintenance of instream flow to support river ecosystems. This regulation has evolved from early river management practices to more advanced, systematic approaches, including the Instream Flow Incremental Methodology (IFIM). Despite these advancements, river management in South Korea, particularly in the Seomjin River Basin, continues to face numerous challenges. In this study, a three-dimensional numerical model was developed to simulate the hydrodynamic and salinity conditions of the Seomjin River Estuary. This study proposes optimal instream flows to support critical habitats for the Corbicula bivalve, which has seen a significant decline due to salinity intrusion by environmental changes. Using the Environmental Fluid Dynamics Code (EFDC), the model simulates salinity and river discharge with calibration and validation by incorporating historical data. Subsequently, this study evaluates how river discharge affects salinity in four major Corbicula habitats (Dugok, Shinbi, Mokdo, and Hwamok). Finally, we determine the minimum flow (instream flow) needed to sustain Corbicula habitats. In short, this study found that the minimum flow rates (instream flow) required to meet target salinities varied significantly across these sites and under different tidal conditions. These findings highlight the necessity of adapting river flow management practices to preserve the ecological health for Corbicula in the Seomjin River Estuary. Furthermore, this study suggests integrating an additional water supply to be used with local water management plans by suggesting short-term and long-term alternatives in order to sustain adapting river minimum flow (instream flow).