<p>Understanding the in-stream total organic carbon (TOC) is becoming increasingly important for water quality management in South Korea. Relative to other water quality variables (e.g., N and P), in-stream carbon dynamics and their responses to climate change have rarely been studied, mainly because of a lack of suitable modeling tools. This study applied the Soil and Water Assessment Tool–Carbon (SWAT-C) model to the Miho River Watershed, South Korea, to investigate the potential changes in in-stream carbon dynamics under climate change. To depict climate change conditions, the projected climatic variables from the global circulation model under four different SSP scenarios were used. This study compared past (1991–2020) and future (2071–2100) in-stream organic carbon to quantitatively represent the impacts of climate change. The results indicated the TOC dynamics differed by SSP scenarios. An increase in future precipitation, particularly in August (55.92–115.17 mm), led to a rise in streamflow from 23.53 m³/s to 33.50 m³/s. Additionally, mean temperatures were projected to rise by 1.26–1.4°C. Interestingly, despite increased precipitation and streamflow, TOC loads during spring seasons were expected to decrease by 5.8–27.27%. This decline was primarily attributed to a reduction in dissolved organic carbon (DOC) from May to July. Warmer conditions promoted vegetation growth, leading to increased DOC uptake by plants. Increased TOC loads during summer seasons were mainly led by increased particulate organic carbon (POC) loads due to precipitation. Furthermore, intensified precipitation resulted in increased resuspension while decreased sedimentation under climate change. This study was the first attempt to anticipate future TOC using a process-based model. The findings informed us of great variability in TOC under climate change, providing valuable information for TOC management strategies under climate change.</p>