Huge subaqueous borrow pits are widely distributed in coast of Japan as a result of dredging action for sandmining or other purposes. In this study, we first review the present status of the borrow pits in whole of Japan. The borrow pits can be classified into two categories: one is the flatten-out type that is typical in Seto Inland Sea, and the other is the depression type that are widely distributed in whole country. The latter type are often steep sided and much deeper than the surroundings. Water circulation inside of the pits is strongly inhibited and organic materials are easily accumulated in the bottom of the pits and therefore, water quality deterioration such as development of severe oxygen depletion is often observed. Therefore, some remediation actions are urgent task to restore damaged ecosystems. Recontouring, which is one of the promising methods to restore the damaged ecosystems, has been conducted in the borrow pits in Mikawa Bay by using maintenance dredging sediments. In the latter half of this paper, we report the outline of the restoration action and main results of a research project which aims to develop evaluation methods to estimate beneficial effects of the recontouring on the coastal environment. In the research project, we successfully developed a comprehensive procedure to predict the response of benthic community structure and their purification function after restoration actions conducted in the Mikawa bay.