Phytoplankton responsible for harmful algal blooms (HABs) may originate from the seed bank present in lake and river sediments. In this study, we investigated the germination of phytoplankton in the laboratory from resting cells in sediments collected during spring from four tributary and littoral zones of Lake Taihu (east, south, west, and north), the season before HABs typically occur. We evaluated the potential for germinated phytoplankton to contribute to HABs. We found that 26 species from three phyla including Cyanobacteria, Bacillariophyta, and Chlorophyta germinated from the sediment during the 15-day incubation experiment. The germinated phytoplankton species from the sediments collected in most areas were moderately or very similar, but dominant species exhibited different temporal and spatial distributions. The densities of germinated cells for different phytoplankton species varied at different times during the incubation period. Cyanobacteria Microcystis spp. (1,511 cells g