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.