Chemical oxygen demand (COD) in Lake Biwa has not been improved during the past quarter century in spite of decreases in organic loadings from watershed and total phytoplankton biovolume. In addition, an increase in cyanobacteria has been observed in Lake Biwa. Most of cyanobacteria have a large volume of gelatinous sheath, which is usually called extracellular polysaccharides (EPS) and may play a significant role in COD in the lake. Therefore, we analyzed long-term variation of phytoplankton biovolume and EPS volume at Imazuoki, Nagahamaoki and Imazuokichuo-points in the northern basin of Lake Biwa from 1980 to 2009. The EPS volume in 2000-2009 increased approximately three times compared with that in 1980-1989 at Nagahamaoki-point, although the phytoplankton biovolume in 2000-2009 decreased to 85% of that in 1980-1989. Furthermore, the ratio of EPS volume to the phytoplankton biovolume at Nagahamaoki-point reached 112 in 2000-2009 while that in 1980-1989 remained 31. At Imazuoki and Imazuokichuo-points, the ratio increased from 41 to 109 and from 40 to 120 during the same period, respectively. These results suggest that the large amount of EPS produced by phytoplankton could be one of the major sources of organic matter in Lake Biwa.