The Primary Production of phytoplanktons produces organic matter in high concentration in eutrophicated Hakata Bay, Japan, even during the winter season in spite of low water temperature. Phytoplanktons are considered to have any biological capabilities to keep activities of photosynthesis under the unfavorable conditions, and this affects water quality of the bay. In this study, seasonal variations in primary production efficiency were predicted by using a simple box-type ecosystem model, which introduced the concept of efficiency for absorption of solar radiation energy in relation to growth of phytoplanktons under the low solar radiation intensity. According to the simulation result of primary production, it was organic pollution comes from dissolved organic carbon (DOC) throughout the year, DOC of which is originated from the primary production of phytoplanktons on biological response of the seasonal variation of ambient conditions.