A gap in our understanding of phytoplankton seasonality in temperate lakes exists mainly due to the lack of information collected during the winter months. We summarized seasonal changes of phytoplankton biomass and taxonomic composition relative to water-column biogeochemical conditions in 6 lakes located on Beaver Island and 1 site in Lake Michigan in close geographic proximity to each other (<20 km apart). A number of physical—chemical parameters (e.g., temperature, DOC) were similar between lakes, but lakes towards the interior of the island had lower pH, alkalinity, and conductivity. Moreover, lakes at the interior of the island supported 2-fold greater phytoplankton-chlorophyll and carbon compared with perimeter lakes, and phytoplankton taxonomic composition differed considerably during the ice-free period (April–December). Interestingly, the winter phytoplankton assemblages were strikingly similar in all 7 lakes, when large populations of phyto-flagellates (Chrysophyceae and Cryptophyceae) occurred under the ice at low light and temperatures < 4 °C. Given the mixotrophic capabilities of these phytoflagellates, we suggest seasonal convergence reflects the community response to under-ice conditions, which promotes the occurrence of an important component of annual phytoplankton biomass.