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A national assessment system for the classification of the ecological status of coastal waters according to the requirements of the EU Water Framework Directive was established in Estonia in the year 2007. The Estonian Phytobenthos Index was used to assess the ecological status of coastal waters based on submerged aquatic vegetation. After the testing period it appeared that the selected method did not respond to anthropogenic pressure in two national water types: the Väinameri and Parnu Bay. During this study new indexes were developed and validated against pressure for these areas. The PCF index was combined from the proportion of perennial species, charophytes, and Fucus spp. This index is suitable for the assessment of the ecological status in the Väinameri area. In Parnu Bay the depth distribution of higher plants and the proportion of opportunistic species showed the strongest correlation with eutrophication variables. These metrics were combined into the HPO index. The class boundaries for assessing the ecological status of water quality were determined for both indexes. The paper describes the calculation of the indexes. [ABSTRACT FROM AUTHOR]