Planktonic diatom composition was investigated in association with environmental factors at bi-weekly and weekly intervals from October 2013 to September 2014 in the Golden Horn Estuary (Sea of Marmara). Sixtysix diatom taxa (50 centrics and 16 pennates) within 32 genera were identified in samples taken during the study period. Chaetoceros species were the most abundant species (30 % of the total number of diatom). The other most common species were Proboscis alata, Rhizosolenia hebetata and Skeletonema marinoi from centrics; Ceratoneis closterium, Nitzschia longissima, Pseudo-nitzschia calliantha and Thalassionema nitzschioides from pennates. The abundance of diatom increased towards the upper estuary, but its species richness decreased markedly. The contribution of diatoms to the total phytoplankton abundance decreased from 60 % to 26 % from the lower to the upper estuary. Some diatom taxa, P. calliantha, S marinoi, T minima and C closterium, formed blooms between May and July, reaching the highest abundances 1.6 x 106, 39 x 106, 13 x 106 and 2 x 106 cells L-1, respectively. Salinity, Sec chi depth, dissolved oxygen and pH values decreased gradually from the lower to the upper estuary, while inorganic nutrient concentrations increased. There was a significant positive correlation between temperature and diatom abundance (p<0.01), while there was a negative correlation between temperature and species richness (p < 0.01). However, salinity, Secchi depth and dissolved oxygen were positively correlated with species richness (p < 0.01). Inorganic nutrients were negatively correlated with diatom abundance (p < 0.01) and species richness (p<0.05). Therefore, the main environmental factors affected the distribution of diatoms along this study area. Thus, diatom assemblages may be considered as a good indicator of changing environmental conditions in such environments.