We estimated the contributions of sedimentation and cell lysis to the loss of two large phytoplankton species (Fragilaria crotonensis and Staurastrum dorsidentiferum) in Lake Biwa. Major loss process differed between species, and large phytoplankton did not necessarily function as a nutrient sink. The spring bloom of F. crotonensis was terminated by nutrient depletion and a subsequent increase in sedimentation rate. Although this species could be occasionally grazed by zooplankton, sedimentation eliminated nutrients from the surface. In contrast, the summer bloom of Staurastrum dorsidentiferum crashed mainly as a result of cell lysis caused by fungal infection within the surface mixing layer, which accounted for more than 75% of the mortality rate of this species. Cell lysis of S. dorsidentiferum may lead to nutrients within the surface mixing layer, supporting the production of bacteria and zooplankton. The different loss process of these two species implies that the function of phytoplankton in material flows cannot be assessed by cell size alone. Fungal parasitism can result in a different fate, which may play an important role in material cycling in lakes.