Macrophytes act as important bioindicators of environmental conditions and long-term changes in water quality allowing their use in studying the dynamics of bottom natural complexes. The purpose of the work is to identify the main hydrophysical and hydrochemical factors leading to changes in the biomass of bottom phytocenoses near Cape Kosa Severnaya. The paper analyzes and summarizes literary sources and results of landscape and hydrobotanical studies (summer 1964, 1997, 2006 and 2017) carried out in the coastal zone between Cape Kosa Severnaya and Cape Tolsty. We used data on water temperature, concentrations of nitrates, nitrites, ammonium, phosphates and total suspended matter in water from 1998 to 2021. We also used simulation results of macrophytobenthos biomass dynamics in the area from 1998 to 2002. Several bottom natural complexes were distinguished in the landscape structure of this area at different periods. Their composition and quantity changed over time. In the Ericaria-Gongolaria phytocenosis (0.5-5 m), by 2006 there was an increase in the biomass of the dominant species characterized by an increase in the proportion of epiphytes. In 2017, there was a restoration of the dominant species, and the total biomass almost tripled. The Ericaria-Gongolaria-Phyllophora phytocenosis (5-10 m) had completely disappeared by 2006, and Dictyota spp. took its place in 2017. The Phyllophora phytocenosis (depths over 10 m) significantly degraded in 1997, and its biomass decreased almost to zero. In 2006, Phyllophora crispa was not recorded at these depths, but by 2017, there appeared separate areas of the bottom where Phyllophora crispa was present, with biomass an order of magnitude lower compared to that in 1964. It was concluded that the recorded transformations of benthic communities were caused mainly by changes in water transparency associated with the content of total suspended matter. To monitor the situation, it is advisable to regularly conduct hydrobotanical surveys at intervals of several years.