Snow governs interaction between atmospheric and land surface processes in high mountains, and is also source of fresh water. It is thus important to both climate scientists and local communities. However, our understanding of snow cover dynamics in terms of space and time is limited across the Hindu Kush Himalaya (HKH) region, which is known to be a climatically sensitive region. We used MODIS snow cover area (SCA) data (2003–2012), APHRODITE temperature data (2000–2007), and monthly long term in-situ river discharge data of the Gandaki (1968–2010), Koshi (1977–2010) and Manas (1987–2004) basins to analyse variations among four basins. We gained insights into short term SCA and temperature, long term discharge trends, and regional variability thereby. Strong correlations were observed among SCA, temperature and discharge thereby highlighting the strong nexus between them. Temporal and spatial snow cover variability across the basins is strongly coupled with the variability of two weather systems: Western Disturbances (WD) and Indian Monsoon System (IMS), and strongly influenced by topography. Manifestation of these variability in terms if downstream discharge can have repercussion to water based sectors: hydropower and agriculture, as low flow seasons is seen affected. This study adds to our knowledge of snow fall and melt dynamics in the HKH region, and intra-annual snow melt contributions to downstream discharges. The study is limited by short span of data and it is desirable to perform a similar study using data representing a much longer time span.