Oxygen consumption by bottom sediment in a eutrophied port and harbor is modeled based on field investigation. The model consists of factors of biological contribution and chemical-physical contribution. It is presented that these factors can be estimated by water temperature and dissolved oxygen above the sea bottom. Through modeling sediment oxygen consumption it is found that a penetration depth of oxygen is a useful parameter to represent sea bottom environment as a remediation. Further, estimation method of penetration depth of oxygen is improved to take into the change of the dissolved oxygen above sea bottom consideration.