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Diagnosis of eutrophication requires evidence of disturbance to the balance of organisms. We describe a tool, the Plankton Community Integrity Index (PCII), derived from the Plankton Index (PI) for tracking change in the seasonal patterns of abundance of diatom and dinoflagellate lifeforms when plotted in state space. The tool uses a nutrient-minimum reference period to interpret PCII values as status indicators, with values close to 1 indicating "High" status and 0.6 a Biological Water Quality Criterion (BioWQC) target set at the "Fair"/"Good" status boundary. It has been applied to Hong Kong marine waters, using data from monthly samples from 1995 through 2021. A preliminary analysis, required for the PI method, confirmed monsoonal seasonality in the diatom lifeform. In 5 of the 9 water bodies examined, PCII time series correlated with those of Total Inorganic Nitrogen (TIN). Since 2020, all Water Control Zones met the operationally defined BioWQC target. [Display omitted] • A Phytoplankton Index is proposed to assess quality of Hong Kong marine waters. • Monsoonal seasonality in the diatom lifeform is confirmed. • The proposed index correlated with Total Inorganic Nitrogen in most water bodies. • All local marine waters meet Biological Water Quality Criterion target since 2020. [ABSTRACT FROM AUTHOR]