The aim of this study is to determine the phytoplankton species found on the shores of Burgaz Island and the basic ecological variables that affect their seasonal distribution between May 2013 and February 2014. Water samples were collected from four stations at six different depths and plankton samples were gathered horizontally and vertically. The analysis of phytoplankton community composition revealed 101 phytoplankton taxa belonging to five classes. As a result of the study, two taxa belonging to the Dinophyceae (Corythodinium frenguellii and Gonyaulax scrippsae) were new records for Turkish coastal waters. Additionally, a taxon belonging to Dinophyceae (Pronoctiluca pelagica) and a taxon belonging to Bacillariophyceae (Nitzschia reversa) were new records for the Sea of Marmara. Prorocentrum micans, was the dominant species throughout all sampling periods. During the study, the highest phytoplankton abundance was observed at 0.5 m depth in May 2013 (138,500 cells l−1) and February 2014 (52,620 cells l−1). Primary ecological variables, such as temperature (9.0–21.5 °C), salinity (15.23–37.22‰) and dissolved oxygen (4.89–15.84 mg l−1), were recorded on each sampling occasion. In addition, nitrite + nitrate–N (NO2 + NO3–N) (0.01–7.37 μg-at N l−1), phosphate (PO4–P) (0.05–51.95 μg-at P l−1) and silicate (SiO4–Si) (0.01–0.20 μg-at Si l−1) concentrations were measured. Chlorophyll a and suspended material values ranged between 0.01–3.17 μg l−1 and 10.0–61.5 mg l−1, respectively. Spearman's rank correlation was used to determine the relationship between phytoplankton species and ecological variables, and Bray–Curtis analysis and Euclidean distance were applied to bring out the similarity between stations.