The intricate interaction between climate and land use changes induces complexities in water balance dynamics amidst global environmental shifts. Substantive impacts are delineated via a case study conducted in the Narayani Basin situated within the Hindu Kush Himalaya region. Quantifying uncertainty for average water yield involves employing Monte Carlo simulation and the Kernel Density Function on SWAT hydrological model output, revealing alterations in water balance components characterized by a generally upward trend and increased variability. The water yield varies spatially and temporally, exhibiting higher uncertainty. Variations in uncertainty specific to each scenario are highlighted, emphasizing the interconnected effects of landscape transformation and climate change. Climate models are categorized into four scenarios, representing wet_cool, wet_warm, dry_cool, and dry_warm. In the Far Future, Wet_Cool scenario (SSP585) exhibits the highest uncertainty in annual water yield (CV: 0.18) with a substantial 167% increase, while minimal uncertainty is seen in the Near Future for SSP245 under Dry_Cool conditions (CV: 0.165) with a modest 9% increase. These results underscore the nexus impact of climate and land use alterations, providing valuable insights for informed decision-making in water resource planning. The study emphasizes considering spatial uncertainties for sustainable water management amid ongoing environmental changes.