The main aim of the research carried out in water area of the Dniester Estuary in 2003-2016 has been to study the phytoplankton as a biological element in accordance with the EU Water Framework Directive (WFD) requirements. It has been shown that phytoplankton distribution in the water area was non-uniform; the «spots of blooming» were forming depending on wind pattern and hydrological situation. From the viewpoint of biomass, big diatoms together with cyanobacteria dominated in the central and southern parts of the estuary in 2008-2016. During 14 years’ period vegetation of 432 microalgae and cyanobacteria species was registered; out of those only 20-35 species reached in different years the blooming level (in view of their biomass). In the comprehensive list of phytoplankton species 16 belonged to the group of harmful algae; 11 cyanabacteria species out of those 16 developed actively all over the estuary thus creating additional threat for ichthyoplankton. The values of indices of phytoplankton species richness and diversity, as well as biomass of algae and cyanabacteria in the past years (after 2010) have tendency to grow. According to the WFD environmental state of the Dniester Estuary was assessed as «good» in 2003-2011, while in recent years the quality decreased reaching the category «satisfactory».