The paper includes the results of green algae investigations, made during 1989-2011 in the major aquatic ecosystems of Moldova: the Dniester river, the Prut river, Cuciurgan, Dubasari and Costesti-Stanca reservoirs. The obtained results are compared with data from previous studies (1956-1988). During the period of 1956-2011, there were identified 308 species and intraspecific taxa of Chlorophyta phylum. Green algae among flora spectrum of algal communities constitute 31-64%. It was reported the reduction of green algae diversity in the past 20 years, influenced by changes in hydrological and hydrochemical regimes of ecosystems due to hydraulic structures on rivers, wastewater discharges and intake of nutrients and toxic substances from water basins adjacent territories. Green algae quantitative parameters from the investigated ecosystems are characterized by large amplitude of space-time oscillations of number and biomass values, that stands out when comparing their values over time (seasonal and multiannual dynamics) and space (distribution of algal communities in different sectors of aquatic ecosystems).