Interactions among physical, chemical, and biological components and processes in Crater Lake result in a complex and dynamic ecosystem. In winter and spring, wind energy mixes the lake to a depth of about 200 m. During this period, episodic sinking of cold water below the depth of 200 m produces an upwelling of nutrient-rich water from the deep lake, a process that has a strong influence on the concentrations of nutrients available to phytoplankton in the euphotic zone. Patterns of upwelling are variable from year to year, and physical data indicate that water from the deep lake is completely mixed with surface water every 1–4 years. Phytoplankton cell biovolume and total chlorophyll are distributed uniformly to the depth of 200 m in winter and spring, at which time maximum rates of primary production occur in the upper 60 m of the water column. The onset of thermal stratification in July is associated with development of a chlorophyll maximum at depths between 100 and 140 m and a downward shift of the primary production maximum to depths between 60 and 100 m. Thermal stratification also is accompanied by a stratified distribution of phytoplankton populations that is characterized by assemblages with low species diversity and high dominance in the epilimnion and assemblages with higher diversity and lower dominance in the metalimnion and upper hypolimnion. Therefore, the thermal properties of the upper 200 m of Crater Lake, and associated changes in light and nutrients with increasing depth, are closely related to structural and functional attributes of phytoplankton assemblages in the water column.