The Vakhsh and Pyandj rivers, main tributaries of the Amu Darya River in the mountainous region of the Pamir Alay, play an important role in the water resources of the Aral Sea basin (Central Asia). In this region, the glaciers and snow cover significantly influence the water cycle and flow regime, which could be strongly modified by climate change. The present study, part of a project funded by the European Commission, analyses the hydrological situation in six benchmark basins covering areas of between 1800 and 8400 km2, essentially located in Tajikistan, with a variety of topographical situations, precipitation amounts and glacierized areas. Four types of parameter are discussed: temperature, glaciation, snow cover and river flows. The study is based mainly on a long-time series that ended in the 1990s (with the collapse of the Soviet Union) and on field observations and data collection. In addition, a short, more recent period (May 2000 to May 2002) was examined to better understand the role of snow cover, using scarce monitored data and satellite information. The results confirm the overall homogeneous trend of temperature increase in the mountain range and its impacts on the surface water regime. Concerning the snow cover, significant differences are noted in the location, elevation, orientation and morphology of snow cover in the respective basins. The changes in the river flow regime are regulated by the combination of the snow cover dynamics and the increasing trend of the air temperature.