Segara Anakan Lagoon and Cibereum River are located south of Java Island, precisely on the border between West Java Province and Central Java. This study aimed to reveal phytoplankton community structure related to water quality. Observations were made in May 2021 at seven locations. Ten liters of water were filtered using a plankton net with a mesh size of 53 μm and preserved using Lugol. The parameters observed were the abundance and composition of phytoplankton, dissolved oxygen, pH, temperature, turbidity, conductivity, total dissolved solids, and salinity. Phytoplankton community structure was analyzed using the Diversity Index, Evenness Index, and Dominance Index. The phytoplankton found consisted of Bacillaryophyta, Chlorophyta, Cyanophyta, Dinophyta, and Euglenophyta. Bacillaryophyta had more diversity of species than other phyla, with an abundance range from 38–4,037 individuals/L. Station 7 (at Cibereum River) had a different phytoplankton composition, with a higher abundance and species number, and Oscillatoria sp. as a dominant species. This station has low diversity and evenness index values (0.649 and 0.054, respectively), and the dominance index close to 1 (0.858) indicated unstable habitat for the phytoplankton community. Dissolved oxygen, pH, conductivity, total dissolved solids, and salinity were lower, while turbidity was higher than other stations.