Rainfall and snow-melt are the major sources of water in the Indian Himalayas. Notable changes in terms of the quantity and space-time characteristics of rainfall and snow-melt over this region have been reported in recent decades. In addition, shift in the cropping systems, urbanization and population growth add additional stress on the available freshwater. These changes significantly modify water runoff and the quality of available freshwater, in turn, disrupting the balance of the regional hydrological cycle through negative feedbacks. So it is the need of the hour to design actionable intervention strategies at policy level for maintaining a sustainable water budget over these regions for long term sustainability of ecosystem and environment. Here we propose to develop an integrated System Dynamic Model to design and test intervention strategies at policy level to evaluate and remediate water stress over these regions at short-term through intervention strategies and long-term through adaptive measures. We have selected two river basins, Kosi water shed and Upper Jhelum river basin, which have undergone major hydrological changes and affecting disaster vulnerability and livelihood of the people of Uttarakhand and Jammu & Kashmir states respectively. The Kosi River experienced drying up of perennial streams (225.85km in 1960 to 41.9 km today), diminishing spring discharge, reduced summer flows and the rising demands over the river ecosystem have put the region under severe water stress. Likewise, the Upper Jhelum basin has also undergone major changes in terms of the hydrological cycle, flood vulnerability and rise in demands of water. Accordingly these basins were selected for the first such exercise with the expectation that i) the outcome will not only address a situation faced by large sections of humanity but ii) also, because of their variegated texture, offer an approach that can be easily adopted for other basins along the Himalaya. Lastly, the high interdisciplinary S & T knowledge and capabilities created in the process as well as the array of instrumentation systems that alert us to adverse changes in the state of the ecological system would hasten the approach of data and knowledge guided approaches to sustainable management.