Three months have passed since the Great East Japan Earthquake occurred. Public infrastructures were largely destroyed by the extreme tsunami. In these affected areas, it is reasonable to consider the grand design of the new land use and public infrastructure rather than restoring to the original state from the viewpoint of disaster prevention. In reconstruction from the Tohoku earthquake, the rehabilitation plan by changing the traditional idea from the long-term view is required that can reduce the damage in case of the next disaster. It is also necessary to reconsider the relationship between environmental conservation and rehabilitation projects. In the coastal region, significant environmental change has been already caused by the tsunami and land subsidence. Leaving a wide habitat in these rivers and coastal areas which will improve the ecological integrity can truly increase motivation and effectiveness of rehabilitation by improving fishery production and tourism value. Therefore, it is necessary to identify, in advance, high potential areas where biodiversity and ecological functions for material cycling will be increased, and reflect them for reconstruction master plan. In this paper, based on the above idea, issues to be discussed in the Ecology and Civil Engineering Society are presented for the reconstruction from the Tohoku earthquake and Tsunami.