This paper provides the results of hydrological modelling in a mesoscale glaciated alpine catchment of the Himalayan region. In the context of global climate change, the hydrological regime of an alpine mountain is likely to be affected, which might produce serious implications for downstream water availability. The main objective of this study was to understand the hydrological system dynamics of a glaciated catchment, the Dudh Kosi River basin, in Nepal, using the J2000 hydrological model and thereby understand how the rise in air temperature will affect the hydrological processes. The model is able to reproduce the overall hydrological dynamics quite well with an efficiency result of Nash–Sutcliffe (0.85), logarithm Nash–Sutcliffe (0.93) and coefficient of determination (0.85) for the study period. The average contribution from glacier areas to total streamflow is estimated to be 17%, and snowmelt (other than from glacier areas) accounts for another 17%. This indicates the significance of the snow and glacier runoff in the Himalayan region. The hypothetical rise in temperature scenarios at a rate of +2 and +4 °C indicated that the snowmelt process might be largely affected. An increase in snowmelt volume is noted during the premonsoon period, whereas the contribution during the monsoon season is significantly decreased. This occurs mainly because the rise in temperature will shift the snowline up to areas of higher altitude and thereby reduce the snow storage capacity of the basin. This indicates that the region is particularly vulnerable to global climate change and the associated risk of decreasing water availability to downstream areas. Under the assumed warming scenarios, it is likely that in the future, the river might shift from a ‘melt-dominated river’ to a ‘rain-dominated river’. The J2000 model should be considered a promising tool to better understand the hydrological dynamics in alpine mountain catchments of the Himalayan region. This understanding will be quite useful for further analysis of ‘what-if scenarios’ in the context of global climate and land-use changes and ultimately for sustainable Integrated Water Resources Management in the Himalayan region. Copyright © 2012 John Wiley & Sons, Ltd.