Abstract <p>The seasonal dynamics of phytoplankton from May to October were studied in the estuarine areas of the spawning rivers Onenusi (2023) and Gorbusha (2024) in the southeastern part of the Tatar Strait. A high species diversity (447) was revealed, including new taxa for the Tatar Strait (<i>Thalassiosira ordinaria</i> Makarova, <i>T. binata</i> Fryxell, and <i>T.</i> <i>pacifica</i> Gran et Angst) and for the seas of Russia (<i>T.</i> <i>kushirensis</i> Takano). The main similarity between both study areas was the sharp spatial heterogeneity associated with the geomorphology of the region. Maximum biomass values (up to 40 g/m³ in the Onenusi River area and up to 15 g/m³ in the Gorbusha River area) were confined to a narrow strip near the water’s edge, where diatoms of the genus <i>Thalassiosira</i> dominated. In the offshore part (at a depth of 5–20 m), the biomass was an order of magnitude lower, but the taxonomic diversity, due to pelagic species, was higher. The main difference was evident in the nature of the seasonal dynamics, determined by meteorological conditions. In the relatively calm year of 2023, a series of intense biomass peaks (up to 3.87 g/m³ on average) were observed near the Onenusi River. These peaks were observed in the second 10-day period of May, the first and third 10-day periods of June, and the third 10-day period of July and were caused by a prolonged diatom bloom. In 2024, characterized by stormier conditions, near the Gorbusha River, the total biomass was lower (up to 1.77 g/m³), and its dynamics were described by a two-peaked curve, with peaks in early June and early July. Increased wind mixing led to an increase in the proportion of dinoflagellates. The obtained results emphasized the need to consider the patchy nature of the environment and the leading role of protected shallow waters when assessing coastal productivity.</p>