<p>Understanding how phytoplankton diversity changes over time and the driving mechanisms behind these changes is crucial for the development of freshwater ecosystem conservation policies. However, few studies have simultaneously explored the temporal patterns of lake phytoplankton diversity in three dimensions: taxonomy, function, and phylogeny. Using 20&#xa0;years (January 1997–December 2016) of plankton monitoring data from Lake Kasumigaura, a temperate lake in Japan, we explored the correlations and ecological drivers between multidimensional temporal beta diversity of lake phytoplankton and their components (i.e., turnover and nestedness). Different dimensions of temporal beta diversity and their components were weakly correlated, suggesting that they provide complementary ecological information. Although temporal beta diversity was found to be primarily driven by stochastic processes, it is worth noting that biotic interactions play a more important role in deterministic processes compared to local environmental and climatic factors. Temporal functional and phylogenetic beta diversity showed a stronger response to deterministic processes compared to temporal taxonomic beta diversity. Our study emphasizes the need for integrated multidimensional biodiversity studies and calls for the incorporation of biological factors in studies of biodiversity drivers.</p>