Following the ‘Volgoneft-248’ oil spill, phytoplankton distribution within the affected area was investigated for two years. Simultaneously measured physical variables such as salinity, temperature, Secchi disc, current speed and direction, and total petroleum hydrocarbons (TPH) were evaluated together with phytoplankton data. At the time of the accident, the TPH concentration in surface water was measured as 2.17 mg l−1 and decreased to 88.5 µg l−1 after five days. In the first sampling period, no diatoms were detected in surface water, while dinoflagellates were dominant in the phytoplankton community. The species composition of phytoplankton changed rapidly in two months and the diatoms increased in terms of abundance and diversity. This indicated that the diatoms might be more sensitive to oil pollution than the dinoflagellates. In comparison with the historical datasets, the low phytoplankton abundance following the oil spill should be considered as the small effect of oil on the phytoplankton rather than natural variability of the ecosystem. High oil concentration in the water column caused stress on the phytoplankton and influenced the species composition negatively depending on the sensitivity of groups and the natural variability of the ecosystem.