The fate of phytoplankton communities in different hydrological and hydrochemical conditions was studied in the middle basin of the Biebrza River (NE Poland). Our results showed that hydrological connectivity significantly influenced phytoplankton abundance in floodplain lakes: minimal abundance was stated in lotic and maximal in lentic waterbodies. Phytoplankton diversity and species richness were related to changes in water levels. During the low-water phase, phytoplankton biodiversity was the lowest in lentic and the highest in lotic lakes. High water levels promoted exchanges in species among waterbodies and the river, which increased biodiversity indices. We concluded that the isolation of any floodplain lake from the river channel deteriorates its trophic conditions. Thus, the decrease in phytoplankton biodiversity in floodplain lakes should be regarded as an indirect feedback of the hydrobionts on the hydrological factors.