Most of enclosed bays in Japan are utilized as the area of marine transportation and fishery activities, owing to the calmness of seawater free from high waves and strong current. The Bays are easily polluted by organic maters mainly due to the industrial and urban sewage. From summer to early autumn, red tides, blue tides and masses of oxygen-deficit water develop. As a result, the quality of the water and the bottom sediment deteriorate. The number of bathing resorts and the prevalence of marine leisure activities such as shell gathering are decreasing year by year. Over the past decade, the fishing industry has also suffered. Consequently, a wide range of methods of remediating polluted bay must be adopted. Several methods for restoring the seawater quality are discussed from the viewpoint of profitability and feasibility.