The Indus River, which flows through China, India, and Pakistan, is mainly fed by melting snow and glaciers that are spread across the Hindukush–Karakoram–Himalaya Mountains. The downstream population of the Indus Plain heavily relies on this water resource for drinking, irrigation, and hydropower generation. Therefore, its river runoff variability must be properly monitored. Gilgit Basin, the northwestern part of the Upper Indus Basin, is selected for studying cryosphere dynamics and its implications on river runoff. In this study, 8-day snow products (MOD10A2) of moderate resolution imaging spectroradiometer, from 2001 to 2015 are selected to access the snow-covered area (SCA) in the catchment. A non-parametric Mann–Kendall test and Sen’s slope are calculated to assess whether a significant trend exists in the SCA time series data. Then, data from ground observatories for 1995–2013 are analyzed to demonstrate annual and seasonal signals in air temperature and precipitation. Results indicate that the annual and seasonal mean of SCA show a non-significant decreasing trend, but the autumn season shows a statistically significant decreasing SCA with a slope of −198.36 km 2 /year. The annual mean temperature and precipitation show an increasing trend with highest values of slope 0.05 ◦ C/year and 14.98 mm/year, respectively. Furthermore, Pearson correlation coefficients are calculated for the hydro-meteorological data to demonstrate any possible relationship. The SCA is affirmed to have a highly negative correlation with mean temperature and runoff. Meanwhile, SCA has a very weak relation with precipitation data. The Pearson correlation coefficient between SCA and runoff is −0.82, which confirms that the Gilgit River runoff largely depends on the melting of snow cover rather than direct precipitation. The study indicates that the SCA slightly decreased for the study period, which depicts a possible impact of global warming on this mountainous region.