The phytoplankton community in the estuarine system is affected by changes of physicochemical factors easily. The present study analyzed phytoplankton community distribution and similarity, in addition to exploring factors influencing variations in phytoplankton community structure in three lakes located in the Yeongsan River estuary from March 2014 to November 2017. We carried out non-multidimensional scaling (NMDS) and random forest analysis (RF) for comparing the pattern of phytoplankton distribution and the relationship between phytoplankton distribution and environmental variables. Similarity Percentage (SIMPER) and Analysis of Similarity (ANOSIM) were performed to figure out the similarity of phytoplankton community at each site of three lakes. From NMDS, Phytoplankton community distribution differed between Yeongsan and Gumho lakes, and the factors influencing the distribution of phytoplankton communities across the three lakes were water temperature, dissolved oxygen, total nitrogen (T-N), nitrate-N (NO₃-N), and conductivity. NO₃-N was a key factor influencing phytoplankton community structure in the three lakes based on RF. A total of 24 species were identified as indicator species in the three lakes studied, with the highest species numbers observed in Yeongsan Lake (13) and the lowest observed in Yeongam Lake (2). According to SIMPER and ANOSIM results, the phytoplankton community in Yeongsan and Yeongam lakes were similar, and they differed from those in Gumho Lake. In addition, the phytoplankton community structure varied across the study sites in the three lakes, indicating that water channels across the lakes a minor influence phytoplankton community distribution.