Highland freshwater ecosystems respond rapidly to changing climatic conditions making the biota of mountain streams and rivers particularly vulnerable to climate change. Lack of data and concepts to monitor and manage the potential effects of climate change on freshwater biota is particularly evident in developing countries. Many of the highest and longest mountain systems are found in these regions and provide fundamental water-based services to these countries. The climate sensitive zone (CSZ) concept is based upon changes in community composition along altitudinal gradients that serve as a proxy for climatic gradients. The CSZ characterizes a community of climatically sensitive biota that is likely to react quickly to climate change. We present a framework on how the CSZ can be adapted to and implemented in streams, and demonstrate its applicability for central Himalayan streams of Nepal. We sampled and analyzed benthic invertebrate communities of 58 central Himalayan streams along altitudinal gradients from 1500 to 4500 m asl. A generalized linear model identified altitude as the only significant, albeit indirect, variable explaining benthic invertebrate composition. We applied species turnover scores and threshold indicator taxon analysis (TITAN) to identify the CSZ in central Himalayan streams along the extensive altitudinal gradients. An altitudinal band between 2900 and 3500 m was identified as CSZ and was characterized by 33 indicator taxa. Identifying CSZs in streams can help prioritize resources for monitoring climate change impacts in running waters and help pinpoint stream reaches suitable for testing the efficacy of climate change-directed mitigation practices.