The key goal of the Water Framework Directive is to achieve a good ecological status in water bodies. The ecological status is mainly determined by the biological elements, which are a very good indicator of the changes taking place in water environments. Thus, this article focuses on the analysis of different methods of assessment of the ecological status of water bodies based on macrophytes used in selected countries in the European Union (the Macrophyte Index for Rivers (MMOR)—Poland; the Mean Trophic Rank (MTR)—Ireland; the Trophic Index of Macrophytes (TIM)—Bavaria, Germany; the Bulgarian Reference Index of Macrophytes (RI-BG)—Bulgaria). Three research sections have been selected for research on the river Ślęza: The reference section, the section above the barrage and the section below the barrage. The analysis carried out revealed considerable similarity between the results obtained by all these methods—the differences were at most by one class of ecological status (and the analysis of sums of Wilcoxon’s ranks revealed that there were no differences between the results obtained using different methods, i.e., p = 0.860). With respect to surface waters, investigation of biological elements is important because it allows one to retrace the past and foresee the future based on the past and present trends in the changes occurring in the species diversity and structure of not only macrophytes, but also other groups of organisms. Further action is required that would determine the scope of influence of barrages with hydroelectric buildings on the environment (in the case of the investigated barrage this influence is negative).
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