More than 140 quantitative zooplankton samples (collected on the left bank of the Prut River during the years 2013 – 2015) were analyzed with the aim to study the current state of zooplankton diversity in the middle and lower sector of this transboundary river. There are some factors that limit survival of zooplankton community in the middle and low sectors of the Prut River: significant turbidity of water and hydrological drought during July-October when the small tributaries dry up and do not reach the river bed, as well as the stagnant waters of the Prut meadow are also drying up.