The purpose of this study was to consider the present status and challenges of aquatic animals inhabiting low-lying plains and mountainous regions in Japanese rural areas and to propose future conservation measures. My conclusions are as follows. On low-lying plains where modernizing agriculture such as farmland consolidation is developed, the development project is pointed out the problems from the viewpoint of the conservation of aquatic animals. My preference is for the irrigation water system to be pipelined and the drainage water system to be open channel. As for the drainage network, year-round water flow and the use of natural materials for canal beds are very important. Mountainous regions have suffered from depopulation, and maintaining terrace paddy fields has been difficult. To use agriculture to fulfill multiple functions, I propose zoning into agricultural land management areas, grass and forest management areas, and native forest areas. Appropriate adaptive management is required both on low-lying plains and mountainous regions. Additionally, it is significant to conserve aquatic animals in the watershed. The components of the watershed include farm ponds, dam reservoirs, lakes, flood control basins, paddy fields, rice terraces, rivers, irrigation canals, and drainage canals. It is also important to ensure water flow in the artificial systems around the paddy fields throughout the year. Using springs and groundwater during non-irrigation seasons is effective and efficient both on low-lying plains and in mountainous regions.