Environmental flow (e-flow) practices were investigated for 100 class A rivers in Japan, which are managed by the central government. We examined how much e-flow requirements (EFRs) are allocated for each river, and investigated the seasonally variable flow components, objectives, and target organisms. The EFRs of the 100 rivers ranged from 5 to 51% as a percentage of the mean annual discharge (MAD). Protecting physical habitat was an e-flow objective for all target rivers.Protecting water quality and cultural scenery, preventing salt damage, and maintaining groundwater levels were also common objectives. However, the minimum flow required for the migration and spawning of 12 representative fish species was the most influential factor. The Japanese e-flow framework is a holistic approach that takes not only individual species but also multiple aspects of ecosystem services, including its social and cultural value, into account. E-flows for all target rivers were given as a form of minimum flow. Eighty-six percent of the rivers considered seasonally variable flow targets, while 14% designed constant minimum flow throughout a year. The reason why the EFRs do not consider natural flow variability is that the storage and control capacity of Japanese dams is minimal, and that problems associated with the modified flow regime is not critical at present. The Japanese e-flow framework has been successfully implemented, and it has been institutionally integrated into river management for 30 years. However, it will require adaptive management and adjustment in the future as social structure, climate, and hydroecological characteristics change.