Different terms have been used to describe the state of river ecosystems. These include the following: hydrological, hydrochemical, bioproductive, sanitari-biological. The present work attempts to characterize the state of a river's ecosystem by analysis of phytoplankton species diversity in the Desna river. The Desna is a typical lowland river. Its system includes tributaries and flood waters of different types and origin. Their biodiversity to some extent determines species composition and abundance of phytoplankton in the bed of the main river. Apart from this, species diversity of algae in some parts of the river is influenced by geographical, hydrological, and hydrochemical factors (climate, depth, stream speed, type of sediments, presence or absence of bends, etc.). The plankton algae community is a complicated system, and its ability to synthesize organic matter depends of many agents. Its structure is an important index of ecosystem stability in the presence of different ecological factors, including man. Results of this work suggest that phytoplankton species diversity in different parts of a river not only contains information about the origin of the water, but also, to some extent, can provide an integral index of the condition of the ecosystem.