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Although the effect of salinity on phytoplankton community structure has been studied in many coastal lagoons at different times, it has not been studied simultaneously in different lagoons that are not on the same delta but are geographically close to each other. In the present study, the effect of temporal and spatial changes in salinity on the phytoplankton biovolume, species richness, diversity, and species composition was investigated seasonally in 2020 and 2021 in 6 coastal lagoons of Marmara Basin (Türkiye). In more saline lagoons, phytoplankton biovolume, species richness, diversity, and the total number of species were lower. In lagoons which salinity values were approximate, the species composition was similar. Although the salinity in the lagoons did not show significant change seasonally, biovolume values were lower in Mert lagoon in the fall of 2020 when the salinity values were higher compared to the spring of 2021. Moreover, the considerable decrease in salinity shifted the dominant species structure from high salinity optima species to low salinity optima species in this lagoon. Other effective parameters in the seasonal distribution of dominant species were detected as temperature, dissolved oxygen, alkalinity, and nitrate nitrogen. [ABSTRACT FROM AUTHOR]