The distribution of phytoplankton diversity and abundance found in coastal areas is usually different from the open seas due to changes in environmental parameters. The study was conducted to provide data on the distribution, diversity (H’ and Simpson’s indices), and abundance of phytoplankton in five different stations and to identify some influencing factors using canonical correspondence analysis (CCA). Three stations (Arowi, Rendani, and Maruni) are inside an embayment area and close to the center of human activity; the other two stations (Sidei and Undi) are off the bay. Total cell abundance ranged from 1,680 to 10,260 cells.m−3. The Baccilariophyceae were the most diverse and numerous classes. There were 17 phytoplankton taxa members of the classes of Bacillariophyceae (11 taxa), Dinophyceae (2 taxa), Chlorophyceae (2 taxa), and Cyanophyceae (2 taxa). The phytoplankton from Arowi station showed highest diversity (H’ = 2.38), followed by Sidey (H’ = 2.24), Undi (H’ = 2.10), Rendani (H’ = 2.06), and Maruni stations (H’ = 1.83). The ecological indices of Arowi, Sidey, Undi, and Rendani indicated quite stable communities, while Maruni was indicated unstable communities. Several species of blooming and toxic phytoplankton were found at all stations, one of which was Pseudonitczhia sp. CCA analysis showed that salinity, temperature, pH, phosphate, and current are limiting factors for the distribution and abundance of phytoplankton in Manokwari waters.