Fish farming using net pens in some Japanese enclosed bays started in the late 1950s and was referred to as “the conversion of catching fisheries to rearing fisheries.” Net pen aquaculture has increased rapidly in popularity in the enclosed coastal areas of Japan since the 1970s. Total yields from net pen aquaculture recently reached approximately 270,000 metric tons, the majority of which is contributed by the culture of yellowtail, salmon, and red sea bream (Shirota 1990, MAFF 2005). A major problem of using net pens that has yet to be solved is that the fish are reared at extremely high densities with limited space and they require large amounts of food. Dissolved oxygen (DO) tends to decrease in the water in the net pens during the night due to respiration of the fish and the cessation of photosynthetic activities of phytoplankton (Hirata and Kadowaki 1990). Only 10% - 20% of the food fed to cultured fish contributes to their somatic growth. The remainder tends to be discharged as waste in the form of organic particles and inorganic nutrients outside the net pens, often causing organic enrichment of the sediment just below the fish farm and eutrophication of the water in the coves and bays where the fish farms are located (Tsutsumi and Kikuchi 1983; Hirata et al. 1994).