The interactions between sensitivity and variability of macrophyte and diatom communities were evaluated as a research support of methodologies required by the Water Framework Directive. Slope and shading were identified as additional typological parameters improving links between unimpacted macrophyte communities and running water types. Two other studies demonstrated indication value of macrophytes for assessment of nutrient enrichment and hydromorphological degradation. The special exercises were realized within the STAR project to evaluate sources of variability/uncertainty in assessment methods based on macrophytes and diatoms. Sampling period and shading of the site were found as major factors affecting variability in macrophyte assessment results. Uncertainty of diatom assessment is predominantly associated with selection of site, substrate type and taxonomic identification. Further extension of indication systems and definition of macrophyte/diatom-specific typology of running waters are considered as the main aims of subsequent investigations.