Oxygen-deficient water kills benthic fauna, and degrades ecosystem function. Recently, borrow pits, caused by the sand mining at the bottom of the sea, have been identified as a source of oxygen-deficient water. Projects that restore borrow pit areas have already been begun in some coastal areas of Japan. In this study, we predicted the improvement of ecosystem functions expected after restoring two borrow pit areas of Mikawa Bay, and examined the cost-effectiveness of the restoration project. Firstly, we examined the relationship between dissolved oxygen (DO) and the biomass of benthic fauna in the sea area around two borrow pits, located in different depths of water in the north-eastern part of Mikawa Bay. As a result, the biomass of benthic fauna can be predicted using a new index: the oxygen-deficient sensitivity index (OSI), which is calculated from DO saturation and water temperature measurements. Secondly, we predicted the biomass of the benthic fauna after the two borrow pits were restored and calculated the expected economic value of ecosystem functions, such as water purification, that improved owing to the recovery of the benthic fauna. We then compared these values with the restoration cost of the borrow pit areas. When we compared the cost-effectiveness of the borrow pits, we found that the effect of restoration was high for the borrow pit in the shallower sea area. Therefore, it is necessary to examine the cost-effectiveness of restoration projects prior to undertaking similar projects.