The Nexus approach plays a critical role in understanding complex system dynamics under climate change and supporting watershed management. As biodiversity is increasingly recognized as a key resource, the Food-Water-Biodiversity (FWB) Nexus has gained importance. However, scalable models that incorporate human activities and biodiversity are limited, particularly in the Republic of Korea. This study aims to develop an FWB Nexus assessment tool by integrating the Soil and Water Assessment Tool (SWAT) with Agent-Based Model (ABM), referred to as SWAT-ABM, and demonstrate its application in the Yeongsan River Basin in Naju-si, Jeollanam-do. The SWAT model was first calibrated using streamflow and rice production data, while the ABM decision-making algorithm was developed through comparative and logical analysis. Biodiversity was assessed in ABM through exceedance probability results from each reach. ABM uses SWAT outputs, including rice and pea production, land use type, irrigation, and streamflow, to update land cover, crop type, and irrigation efficiency at the HRU level. Three FWB Nexus management scenarios, combined with SSP-1.26 and SSP-5.85, were tested from 2024 to 2050. The scenarios’ effectiveness and fairness based on FWB Nexus were compared based on the spatial and temporal distribution of rice production, irrigated water, and streamflow. Model performance was assessed using R², NSE, PBIAS, and KGE, with values of 0.58, 0.08, 77.3, and -0.18, respectively. Although there was high bias in estimates, the model still captured overall trends. Scenario results indicate that streamflow concentration increases under worsening climate change, exacerbating trade-offs within the FWB Nexus, particularly the imbalance of water resources during the farming season. The most effective management measure in a short- and mid-term were irrigation efficiency improvement compared to other two measures, although afforestation and crop conversion also contributed to enhancing synergies. This study demonstrates the potential of SWAT-ABM as a decision-making tool in watershed management considering the FWB Nexus, while highlighting challenges such as model performance, temporal resolution, and ABM complexity. Keywords: FWB(Food-Water-Biodiversity) Nexus, SWAT, ABM (Agent-Based Model), Watershed management, Climate changeAcknowledgments: This paper was supported by Technology Development Project for Creation and Management of Ecosystem based Carbon Sinks (project number) through KEITI, Ministry of Environment, and the framework of international cooperation program managed by the National Research Foundation of Korea (No. 2021K2A9A1A02101519).