Abstract <p>Freshwater phytoplankton is sensitive to environmental changes; therefore, its monitoring is a crucial aspect of ecological, recreational, and economic importance. Study of the long-term dynamics of phytoplankton populations is of paramount importance, as it enables elucidating the factors causing this dynamics and makes it possible to propose scenarios for the future. The dynamics of the dominant species of summer phytoplankton was studied in the Velikaya River delta in 2016–2021, and the effect of the changes in pH and water temperature on the species composition and the quantitative characteristics of phytoplankton was analyzed. In general, both the species diversity and the phytoplankton abundance tended to decrease in the Velikaya River delta during the study period. In 2020 and 2021, there was a sharp decline in the abundance/biomass of the phytoplankton species that usually dominated in the river. These changes first affected green microalgae and cyanobacteria (2020), and then diatoms (2021). During the same period (2020–2021), the largest decrease in abundance was observed in the cyanobacteria <i>Aphanocapsa delicatissima</i>; this allowed us to consider this species as an indicator of the phytoplankton community status in the Velikaya River delta. The water temperature and pH significantly influenced the abundance of the dominant phylums (Bacillariophyta, Chlorophyta, and Cyanobacteria), but correlated weakly with the species composition. In particular, water temperature and pH influenced the cyanobacteria abundance, indicating the importance of these factors in the initiation of phytoplankton blooms in the water bodies and suggesting that the influence is enhanced by their combined effect.</p>