Climate change in the Himalaya is already affecting local social-ecological systems. Therefore, adaptation to changing climate has become crucial. This study explores the adaptation efforts made and barriers faced by the farmers of the three different ecological zones within the Kaligandaki Basin, Nepal: the Trans-Himalaya, the Middle-Mountain, and the Tarai. Information was collected through face-to-face interviews in 360 households, 21 Focus Group Discussions, 63 Key Informant Interviews, and sketches of 12 Crop Calendars. Major adaptation strategies adopted at varying degrees by the households were observed in relation to changes in cropping systems; management of farmland, water and livestock resources; occupational changes; and migration. However, adopted strategies have produced both positive and negative results, increasing the uncertainty amongst farmers. Flood controls, occupational changes, and labour migration abroad have produced positive results in livelihood security. Conversely, farmers are hesitant to invest in agricultural adaptation strategies because increased investment also increases the financial risk with the potential of little improvements in physical conditions. The lack of irrigation, lack of reliable weather forecasts, lack of adaptable seeds varieties, increased inter-annual variability in climate system, poor external supports, household's weak economy and poor adaptation knowledge, and decreased interest of younger generations in agro-livestock activities are identified adaptation barriers. Further, occupational changes and labour migration have negatively affected agro-ecology and agro-economy. The uncertainty in adaptation observed in the Nepalese social-ecosystems, which are already at the edge of sustainability threshold, is further leading towards vulnerability. Yet, communities’ needs are not being addressed by national adaptation policies.