We examined the seasonal changes in cell size and abundance of the dominant diatoms Aulacoseira ambigua f. japonica, Aulacoseira granulata, and Fragilaria crotonensis, together with environmental variables, in the northern basin of Lake Biwa. The cell size of the diatoms decreased gradually with the increase in cell abundance, indicating that the population underwent vegetative reproduction followed by sexual reproduction. The observation revealed two diatom blooms in a year. The autumn bloom from early October to late November was primarily dominated by A. granulata, A. ambigua f. japonica, and F. crotonensis. The minimum cell size of the diatoms recorded was 30, 20, and 75 μm, respectively. F. crotonensis caused another bloom from late March to early May; the minimum cell size recorded was 68 μm. These results suggested that F. crotonensis undergoes sexual reproduction twice a year, while the other two diatom species undergo sexual reproduction once a year. Correlation matrices and redundancy analysis were performed to explore the relationship of various environmental factors to cell size reduction and restoration of the seasonally dominant diatoms, and it is suggested that water temperature and/or concentration of dissolved inorganic nitrogen are critical environmental variables for seasonal changes in cell abundance and/or size of the dominant diatom species. Our results demonstrated that each diatom species had distinct favorable ecological conditions for staging its life cycle.