A precise estimation of seasonal runoff and accurate quantification of discharge components is imperative for understanding the hydroclimatic regimes in mountainous regions. This study aimed to investigate daily discharge processes and seasonal runoff composition by employing a temperature-index Snowmelt Runoff Model (SRM) using in-situ hydro-meteorological data and limited field observations with a combination of remote sensing data in the debris-covered and clean-ice glaciers. This analysis showed that meltwater production was reduced by 26.5% considering clean-ice and debris-cover ice scenarios necessitating the importance of incorporating debris cover and debris thickness information in temperature-index and snowmelt runoff models. The simulation of daily discharge shows satisfactory agreement with the coefficient of determination (0.89–0.91) and the Nash–Sutcliffe Efficiency (0.85–0.88) for the calibration (2001–02) and validation (2003–10) periods, respectively. Decadal analysis of supraglacial debris-covered area changes shows a 0.37% increase per year on average exhibiting negligible effect on glacier melting and associated flow regimes. Analysis of MODIS snow cover data revealed that the seasonal snow cover varies between 80% in winter and 30% in summer. Negative trends in the snow cover were observed during winter and slightly increasing trends during summers indicated a decreasing influence of westerlies and a strengthening of the Indian summer monsoon system over the region.