Technical regulations for the lower Vistula River made in the 19th century created a number of shallow reservoirs. The reservoirs are diverse: they can be permanently connected to or disconnected from the main channel of the river. Medium and low water levels of the Vistula cause the reservoirs to not have even a temporary connection to the river. In May 2010 the flood that occurred on the Vistula flooded all the investigated reservoirs. The aim of our study was to learn about the influence of catastrophic flooding on the zooplankton community in the studied floodplain lakes. The study compared the results of zooplankton investigations before the flood (July and August 2009) with results after the flood (July and August 2010). The flood destroyed submerged plants and brought suspension, which changed abiotic conditions of life in the floodplain lakes. The flood waters caused a decrease in the number of species and rebuilt the structure of zooplankton species in the reservoirs. The increase of rotifer species at the expense of crustaceans was observed at different sites. There was also a several-fold increase in the abundance of zooplankton. The largest changes of zooplankton after the flood were recorded in the floodplain lakes that were rich in submerged vegetation (before the flood).