In the years 2007–2015, phytoplankton of six floodplain lakes of the Lower Vistula were studied. During this period, river levels were recorded ranging from normal to both extremely high and extremely low. The research attempted to answer two questions: (i) Do the distributions of phytoplankton communities differ between different types of floodplain lakes? (ii) How are the phytoplankton in floodplain lakes affected by extreme hydrological phenomena? The floodplain lakes were divided into the following types: those connected with the river in a turbid state; and those isolated with pleustophytes and/or elodeids. During the research period, a total of 477 species of phytoplankton were found in the floodplain lakes, most of which belonged to diatoms or chlorococcal green algae. Those lakes connected with the river were in a turbid state, and were richer in species, as well as having the highest biomass of phytoplankton. Isolation from a river has always been associated with low phytoplankton biomass, low chlorophyll a concentration, and increased water transparency due to the presence of macrophytes. Extreme hydrological phenomena such as flash floods or prolonged droughts caused alternations in regime from clear water to turbid, or vice versa.