Recent research has showed increasing interest at the vital role of irrigation ponds that plays at biodiversity conservation, and provides ecological functions at a wide range. However, many irrigation ponds were abolished due to the economic and societal transformation in the rural. In particular, small-scale ponds were abolished and rebuilt to other public uses based on the consensus building process among the community. At the same time, civil organizations also launched initiatives to conserve irrigation ponds for its ecological significance or landscape scenery. However, study pertinent to the small scale ponds in the rural setting is largely neglected. This research aims at revealing the current situation of the utilization and management of small irrigation ponds using a case study of Noto Island in Ishikawa Prefecture. It was found that irrigation ponds are still under the traditional co-management of rural community. The most important finding in this study is that the traditional management of pond water use largely contributes to mitigate the harvest loss from natural disasters such as drought in the face of extreme climate. However, irrigation ponds are facing the threat of degradation due to the sharp decrease of farm population and the existing large number of part time farmers. Therefore, the small scale irrigation ponds and pertinent management and water use allotment should be revalued for its functions at a wide range from the biological and ecological functions and human knowledge system to mitigate disaster threats.