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The aim of the study was to compare the patterns of development of macrophytes and macroinvertebrates in different types of reference mountain rivers. The study is based on reference river sites surveyed throughout the mountains in Poland and Slovakia in two European ecoregions (9—Central Highlands, 10—The Carpathians). A wide range of environmental variables were estimated, including water chemistry, hydromorphology, geology, and the spatial factor. Based on the Jaccard index, macrophyte and macroinvertebrate variation was confirmed between four mountain and upland river types. It was found that the biological diversification is mainly influenced by geological and associated chemical factors. In the case of macroinvertebrates, additionally, the importance of the spatial factor was revealed (difference between ecoregions). Finally, the habitat preferences of various taxa were identified. It was found that extreme mountain conditions can sometimes distort bioindicative response, as was detected in the case of macroinvertebrates in the highest mountain sites. We concluded that consideration of two groups of organisms enables more comprehensive and reliable monitoring than assessment based on a single group, especially when standard bioindicative methods can be distorted by extreme local conditions. [ABSTRACT FROM AUTHOR]