The impact of climate change (CC) on water resources is likely to affect agricultural systems and food security. This is especially critical in a least developed country (LDC) like Nepal where a high percentage of the population is dependent on agriculture for its livelihoods. It is, therefore, crucial for Nepal’s leaders and resource managers to draft and begin implementing national adaptation plans. In order for such planning to be effective, it is critical to gain a more comprehensive understanding of the anticipated impacts of CC and the institutions potentially involved in the adaptation process. This working paper aims to create a more comprehensive understanding of how the impacts of CC will be realized at different scales in Nepal, from household livelihoods to national food security, and the many institutions governing the ultimate adaptation process. Recommendations for adaptation to be effective include a need for a comprehensive effort, involving integrated national planning across all sectors and new infrastructure development (e.g., irrigation, hydropower) to account for longer term impacts of CC. For autonomous adaptation, the focus must be on building and expanding basic infrastructure at the local level which will help provide greater income diversification and access to markets. Such infrastructure will also allow for greater interconnectedness between isolated communities, national government institutions and non-governmental organizations (NGOs). For many local communities, adaptation and development will thus be synonymous because as incomes become more diverse and livelihoods improve, so will resilience towards climate shocks. Fundamental failures of governance and institutional effectiveness must be overcome in order for basic development, and especially for effective strategic adaptation planning and implementation, to occur. Capacity building on CC impacts within the various government departments and ministries is advocated. Furthermore, developing water management strategies as well as agricultural diversification plans, which focus on the increasing variability and uncertainly in water supplies, is also seen as being critical.