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The current study investigates the joint impact of projected land use/land cover change (LULCC) and climate change on the discharge of river Puthimari using Soil and Water Assessment Tool (SWAT). Puthimari, flowing through part of Bhutan and the northeastern region of India, earns its significance by contributing a fairly huge amount of discharge to the mainstream Brahmaputra causing frequent floods downstream, specifically in the monsoon season. The analysis was carried out from 2025 to 2099, by dividing this entire period into three sub-periods, 2025‒2049, 2050‒2074, and 2075‒2099, each of 25 years duration. To evaluate the impact of climate change, this study considered future climate data of five different CMIP5 (Coupled Model Intercomparison Project) climate models and their ensemble for RCP4.5 and RCP8.5 (Representative Concentration Pathways). The changes in LULC were incorporated by projecting the future LULC for 2035, 2065, and 2085 for each of the periods using the CA (Cellular Automata)-Markov model. SWAT performed well for both calibration and validation. The respective Nash-Sutcliffe efficiency (NSE) values for calibration and validation were found to be 0.74 and 0.77. Also, 0.75 and 0.79 coefficient of determination (R 2 ) values were obtained for calibration and validation, respectively. The analyses reveal a 19.76% increase in rural settlement, and a 6.30%, 16.45%, and 8.76% decrease in forest, cropland, and waterbodies in the watershed by the end of this century. The average monsoon rainfall would increase by 14.16% and 38.92%, with a corresponding increase in discharge by 34.27% and 64.67%, under RCP 4.5 and RCP 8.5, respectively. This comprehensive study represents a pioneering effort to thoroughly analyze the future hydrological dynamics of the Puthimari River. This research serves as a vital resource for policymakers and government agencies, offering valuable insights to guide both structural and non-structural measures aimed at safeguarding the river from potential flood devastation. Additionally, it provides essential information to support the implementation of effective watershed management practices., (© 2024. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)