Anthropogenic and natural disturbances have impacted the health of freshwater ecosystems throughout the Hindu Kush Himalayan region. Hydropower development has caused a decline in the connectivity and environmental flows (e-flows) of rivers. To minimize these impacts, the Government of Nepal recently endorsed the Hydropower Environmental Impact Assessment manual. Following its launch, an in-depth training needs assessment revealed that it was necessary to improve stakeholder capacity in freshwater ecosystem assessment for its effective implementation. In this regard, ICIMOD and its partners organized a four-day workshop in November 2019 on assessing freshwater ecosystems as part of environmental impact assessments in Nepal’s hydropower sector.