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The dataset was categorised according to the baseline ecological status assessment of the respective water bodies under the Water Framework Directive (WFD). Species diversity and richness were characterised using the Shannon diversity and species richness indices, respectively, and were analysed for three pre-defined substrate types, three depth zones and three sample-size categories, and the significant categories were statistically validated. Good Environmental Status (GEnS) threshold and reference values were established for the valid combinations of categories denoted as 'ecotypes' through the use of a boxplot and an analysis of variance. The limitations and specifications for an overall GEnS assessment using the above indices are highlighted based on the WFD experience. For the ratio of sensitive species to tolerant species, the BENTIX index classification scale is proposed for GEnS assessment, and an integrated approach to the assessment of diversity and species richness is suggested. 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