Assessment of the Kuchurgany Estuary waters’ trophic status was performed using TSI and TRIX indices based on results of the surveys carried out in 2006-2017; concentration of chlorophyll ‘a’ and bacterioplankton content were also estimated. Practical coincidence of the results of trophic status determination using different methods was shown; this evidenced that practically in all the years the trophic status of waters in the entire estuary did not go below ‘eutrophic’. At that, water quality in the northern part of the estuary, where hypertrophic status was generally registered, had always been of the lowest quality. In 2016-2017 significant increase of the estuary waters’ trophic status was observed, which showed degradation of its ecosystem quality. Urgent measures are required to restore the Kuchurgany Estuary ecosystem.