Taxonomic composition and production dynamics of phytoplankton assemblages in Crater Lake, Oregon, were examined during time periods between 1984 and 2000. The objectives of the study were (1) to investigate spatial and temporal patterns in species composition, chlorophyll concentration, and primary productivity relative to seasonal patterns of water circulation; (2) to explore relationships between water column chemistry and the taxonomic composition of the phytoplankton; and (3) to determine effects of primary and secondary consumers on the phytoplankton assemblage. An analysis of 690 samples obtained on 50 sampling dates from 14 depths in the water column found a total of 163 phytoplankton taxa, 134 of which were identified to genus and 101 were identified to the species or variety level of classification. Dominant species by density or biovolume included Nitzschia gracilis, Stephanodiscus hantzschii, Ankistrodesmus spiralis, Mougeotia parvula, Dinobryon sertularia, Tribonema affine, Aphanocapsa delicatissima, Synechocystis sp., Gymnodinium inversum, and Peridinium inconspicuum. When the lake was thermally stratified in late summer, some of these species exhibited a stratified vertical distribution in the water column. A cluster analysis of these data also revealed a vertical stratification of the flora from the middle of the summer through the early fall. Multivariate test statistics indicated that there was a significant relationship between the species composition of the phytoplankton and a corresponding set of chemical variables measured for samples from the water column. In this case, concentrations of total phosphorus, ammonia, total Kjeldahl nitrogen, and alkalinity were associated with interannual changes in the flora; whereas pH and concentrations of dissolved oxygen, orthophosphate, nitrate, and silicon were more closely related to spatial variation and thermal stratification. The maximum chlorophyll concentration when the lake was thermally stratified in August and September was usually between depths of 100 m and 120 m. In comparison, the depth of maximum primary production ranged from 60 m to 80 m at this time of year. Regression analysis detected a weak negative relationship between chlorophyll concentration and Secchi disk depth, a measure of lake transparency. However, interannual changes in chlorophyll concentration and the species composition of the phytoplankton could not be explained by the removal of the septic field near Rim Village or by patterns of upwelling from the deep lake. An alternative trophic hypothesis proposes that the productivity of Crater Lake is controlled primarily by long-term patterns of climatic change that regulate the supply of allochthonous nutrients.