To provide an underwater ecosystem restoration method for river capable of creating healthy ecosystem based on food chain by developing various habitat environment which permits the movement of aquatic life freely to upstream and downstream areas by repeatedly constructing deep bog sections and shoal sections.

This method comprises a first step for building an upstream interception wall 1 in such a manner that both the bottom of a river and the top surfaces 2, 3 of the wall 1 are located on the same level; a second step for building a down stream interception wall 5 having the level of the top of the wall 5 as same as that of the bottom of the river at a location separated by a predetermined distance from the upstream interception wall 1; and a third step for creating a reservoir 7 for breeding various underwater aquatic life suited to the site characteristics by the dredging at the site to a depth predetermined by a river water depth planning between the upstream interception wall 1 and the down stream interception wall 5, and thereafter the first step to the third step are repeatedly carried out as required between a plurality of bog sections along the river.