For the first time, the paper presents data on the interannual dynamics of quantitative indicators of macrophytoenthos. A comparative analysis of spatiotemporal changes in the contribution of dominant macrophyte species in the western part of Sevastopol Bay over a 40-year period was performed. Hydrobotanical studies were carried out in the summer period of 1977, 2008 and 2017 on the same transects using standard methods. It was revealed that during the period under study, polydominant phytocommunities were formed in the composition of bottom vegetation, dominated by species inhabiting highly eutrophic environments, with a high proportion of epiphytic algae and an insignificant role of Gongolaria barbata. Over the studied period, the lower boundary of macrophyte growth rose and a sharp decrease in macrophytoenthos biomass was registered at a depth of over 5 meters. It was established that changes in the distribution and composition of bottom vegetation in the western part of the bay were caused by its geo-ecological state, which depends on the impact of anthropogenic and natural factors. The construction of hydraulic structures in the bay leads to redistribution of sea grasses growing on soft soils and algae occurring on a hard substrate. It was revealed that after extreme storms, the vegetation cover is predominated by seasonal and annual algae species, with only juvenile Gongolaria barbata beds observed at a depth of 0.5–1 m. The obtained results can be used to monitor the ecological situation in the bay and to organize the coastal-marine nature management.