<p>The Western Ghats, a critical component of southern India’s hydro-climatic system, significantly influence the region’s streamflows. Despite the importance of understanding the impacts of land use/land cover (LULC) changes and climate change (CC) on hydrological indicators, detailed investigations into their effects on flow quantiles remain limited. This study addresses this gap by evaluating the independent and combined impacts of LULC and CC on streamflows and assessing the flow quantiles in two distinct catchments, Aghanashini and Gurupura. We evaluated the changes in future water balance components under two Shared Socioeconomic Pathways (SSPs) climatic scenarios: SSP2-4.5 and 5-8.5. We found that the developed hydrological model performance was reliable, with R², NSE, and PBIAS values ranging from 0.80 to 0.96, 0.76 to 0.94, and − 4.83 to 24.36, respectively, across calibration and validation for the Aghanashini and Gurupura rivers. We also found a 2.38% annual streamflow increase in Gurupura River flow by 2100 due to LULC changes, with negligible impact on Aghanashini River flows. Results showed that the combined effects project a 39.1% runoff decline in Aghanashini and a 3.2% streamflow increase in Gurupura in the far future (2071–2100), with urban downstream areas most affected. Flow quantile analysis for the Aghanshini catchment showed that median flows are expected to rise by 49% and agricultural water availability (Q70) by 21.4% in the far future. Given their potential effects on broader water balance components, these results highlight the need for adaptive water management strategies and underscore the importance of not overlooking LULC changes.</p> Graphical Abstract <p>The graphical abstract illustrates the contrasting hydrological responses of two Western Ghats river basins (Aghanashini and Gurupura) to climate change (CC) and land use/land cover (LULC) alterations. This visual representation summarizes the comprehensive assessment of independent and combined impacts of these factors on streamflow dynamics upto 2100. The results indicate a substantial projected decline in streamflow for the forest-dominated Aghanashini basin (39.1% under RCP 8.5), whereas the agriculture and urbaninfluenced Gurupura basin exhibits a modest increase (3.2%). Flow quantile analysis reveals substantial shifts in water availability patterns, with median flows projected to increase by 49% and agricultural water availability (Q70) by 21.4% in the far future (2071-2100). Seasonal flow variations indicate decreasing monsoon flows (-20%) countered by significant increases in winter (+78.9%) and summer (+87.8%) flows. These findings highlight the differential buffering capacity of diverse landscapes against hydroclimatic stressors and underscore the necessity for adaptive water management strategies tailored to basin-specific characteristics. The graphical abstract effectively communicates these complex ecohydrological interactions, providing a concise visual framework for understanding watershed vulnerability and resilience in this ecologically sensitive region under projected environmental changes.</p>