Assessing runoff under changing land use/land cover (LULC) and climatic conditions is crucial for achieving effective and sustainable water resource management on a global scale. In this study, the focus was on runoff predictions across three diverse Indian watersheds—Wunna, Bharathapuzha, and Mahanadi—spanning distinct agro-climatic zones to capture varying climatic and hydrological complexities. The soil and water assessment (SWAT) tool was used to simulate future runoff influenced by LULC and climate change and to explore the related sustainability implications, including related challenges and proposing countermeasures through a sustainable action plan (SAP). The methodology integrated high-resolution satellite imagery, the cellular automata (CA)–Markov model for projecting LULC changes, and downscaled climate data under representative concentration pathways (RCPs) 4.5 and 8.5, representing moderate and extreme climate scenarios, respectively. SWAT model calibration and validation demonstrated reliable predictive accuracy, with the coefficient of determination values (R²) > 0.50 confirming the reliability of the SWAT model in simulating hydrological processes. The results indicated significant increases in surface runoff due to urbanization, reaching >1000 mm, 600 mm, and 400 mm in southern Bharathapuzha, southeastern Wunna, and northwestern Mahanadi, respectively, especially by 2040 under RCP 8.5. These findings indicate that water quality, agricultural productivity, and urban infrastructure may be threatened. The proposed SAP includes nature-based solutions, like wetland restoration, and climate-resilient strategies to mitigate adverse effects and partially achieve sustainable development goals (SDGs) related to clean water and climate action. This research provides a robust framework for sustainable watershed management in similar regions worldwide.