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When attempting to address the environmental problems of a catchment, it is important to consider changes in a long-term environmental context. However, the long-term data on the state of the environment that are required for such an examination are rarely documented. Such data collection typically requires several years of investigation and observation. In addition, as there may be a significant time lag between the occurrence of a phenomenon and its cause, subsequent environmental investigations of changing animal and plant states scaling up to 5 years may be inadequate. We conducted a long-term analysis of the environmental changes in five sub-catchments of the Nagara River, Japan, assessing a period of 30 years, using a questionnaire survey approach involving local communities. Four sub-catchments of the Yoshida River were also analyzed for comparison. In addition, we attempted to clarify the relationship between various environmental factors and the space–time response of animals and plants. The survey included eight topics: assumed information, hydrological characteristics, habitat conditions for living things, forest state, land cover conditions, river awareness, free-entry information, and respondent information. Our method also has academic significance in that it validates the environmental agent extraction technique using a questionnaire survey. Our results identify management strategies for minimizing biodiversity loss due to climate change. Forest management and human activities should be undertaken with care, and the environmental context going forward into the next century should be considered for integrated catchment management. Elsewhere, reduced greenhouse gas emissions, a much expanded network of protected areas, and/or efforts to provide corridors to ease species movements may be necessary at the global level.
