Problem statement:The Caspian Sea ecosystem has been suffered with many problems since 1980s. Aanthropogenic pollution from heavy metals, hydrocarbons, pesticides, changes in the quantity of nutrient inputs by rivers, are significant threats to biodiversity and biological resources such as plankton structure in the Caspian Sea. According to the significant of phytoplankton community in marine system. The state of the fluctuations of phytoplankton communities of the southwestern Caspian Sea was investigated and compared with the findings of before 2006. Approach: Phytoplankton abundance and species composition of the Caspian Sea were evaluated by using samples collected at 12 stations along three transects. The study revealed that diatoms were higher than other groups of phytoplankton in 2006. The hydrology variation, increased fresh water inflow via rivers and a rise in nutrients concentrations have played important roles in blooming of phytoplankton species, e.g., the diatoms in this study, which is also known from other marines. Similar studies on determination of the effects of environmental degradation on phytoplankton and hydrological processes should be taken into account in near future.