Spatial–temporal variability of phytoplankton community and potentially harmful species in the Golden Horn Estuary (Sea of Marmara) was investigated from October 2018 to September 2019 together with some environmental factors. A total of 148 phytoplankton taxa were identified during the study period. Among these, 134 taxa (90.5%) consisted of diatoms (71 taxa, 48%) and dinoflagellates (63 taxa, 42.5%), while 14 taxa (9.5%) were other groups. Seventeen species were recorded for the first time in the study area. Species richness was highest in October, while it was lowest in August. The species diversity (H') varied according to sampling stations. Cell abundances were higher especially in the middle and upper estuary in spring and summer than in autumn and winter. The abundance of diatoms and euglenophyceans was highest in spring, while the abundance of raphidophycean and cryptophycean was highest in summer. Temperature was correlated positively with total abundance (P < 0.01), but negatively with species diversity (H') (P < 0.01). Several dense algal blooms causing discolouration in surface water occurred in spring and summer. A total of 12 microalgae species known as potentially toxic were detected during this study period. Among these, dinoflagellates Alexandrium cf. tamarense and Dinophysis infundibulum were recorded for the first time in the study area. The increase in species diversity and richness in the upper estuary, and the decrease in frequency of bloom events compared with the previous years indicated the changes in environmental conditions in this study period. Findings showed that phytoplankton might be used as an indicator of the changing environmental conditions in such ecosystems.

Changes in phytoplankton composition of the Golden Horn Estuary were investigated following remediation, through seawater transfer from the Strait of Istanbul to the estuary. Average values of Secchi depth, salinity and dissolved oxygen increased during this study when compared with a previous study. The average number of species (S) and species diversity (H′) increased and they correlated positively with Secchi depth, salinity and dissolved oxygen. There was a similar phytoplankton group composition between this and a previous study, however, the species composition differed. A total of 127 taxa consisting of diatoms (66 taxa), dinoflagellates (49 taxa) and others (12 taxa) were identified. Abundance of dinoflagellates and phytoflagellates and their relative contribution to the total phytoplankton abundance increased during this study, however, the abundance of diatoms and their relative contribution decreased notably, as compared with the previous study. There was a significant positive correlation between salinity and dinoflagellates and phytoflagellates (P < 0.01), and also between Secchi depth and dinoflagellates (P < 0.01) in the upper estuary. Additionally, salinity and Secchi depth correlated positively with species diversity (H′) and number of species (S) (P < 0.01). The increase in water transparency probably contributed to the increase in abundance of dinoflagellates and phytoflagellates. The results revealed that water transparency was one of the most important factors affecting phytoplankton composition in the study area. Changes in some environmental conditions following seawater transfer appear to have changed phytoplankton composition. As a result, phytoplankton species were confirmed as a very good indicator of changed environmental conditions.