Human activities and climate change are key factors impacting ecosystem functions and its goods and services, which are important to the livelihoods of mountain communities. In Nepal, community based ecosystem management has been widely adopted as a way to secure local management and empowerment, but local knowledge, perceptions and values of ecosystem change and services are often ignored, and perhaps inadequately understood, in decision-making processes at district or national level. Our objective therefore was to develop a multi-method approach to support mapping of ecosystem services and assessing their local values. Local perceptions of ecosystem use, change and values were identified using participatory mapping, key informant and focus group discussions, and an extensive household survey carried out in the upstream Koshi River basin. Results were cross-validated with scientific literature, statistics and remote sensing data. Key ecosystem services identified are water, agricultural produce, and various forest products, most of which show a declining trend. We demonstrate that the use of different methods and levels of input results in different and complementary types of insights and detail needed for balanced and informed decision-making regarding sustainable management of ESs to secure current and future livelihoods and ecosystem functioning.