One of the important tools to evaluate the ecological quality of surface water is the Macrophytes indices based on the bioindication capacity of aquatic plants. In Mediterranean rivers (France, Spain, and Portugal), the development of some macrophytes indices like l’Indice Biologique Macrophytes Rivières (IBMR), the biological metric score (BMS), as well as the Fluvial Macrophyte Index (IMF) are founded on the determination of the indicator values of the floristic reference lists. The aim of this study was to test the impact of the eco-Mediterranean differences (from one country to another) on the indicator taxa by comparing the indicator values of the Euro‐ Mediterranean macrophyte indices. With this in mind, we explore the possibility of the introduction of the Euro‐Mediterranean macrophytes-based indices in Morocco (i.e. the hydrological basin of Sebou (HBS)) as a part of a preliminary attempt to develop the first Afro-Mediterranean macrophyte index. We confirm that the ecological amplitude and species optima vary between Mediterranean ecoregions, and indicator taxa differ between countries: There are medium to small correlations between Mediterranean indices: IBMR/BMS (p = 0.000, R2 = 0.57), IMF/BMS (p = 0.000, R2 = 0.34), and IBMR/IMF (p = 0.000, R2 = 0.30). Five species exhibit major differences in indicator values: Zannichellia palustris and Potamogeton pectinatus have more eutrophic indicator values in France (IBMR) than in Spain (IMF). Potamogeton nodosus, Amblystegium riparium and Lycopus europaeus have broader ecological amplitudes in Portugal (BMS) than in France (IBMR) and in Spain (IMF), where it is restricted to eutrophic conditions. Furthermore, the three indicator systems include different indicator-taxon numbers. The comparison of the HBS elaborated list with the Euro‐Mediterranean indices revealed the low level of common taxa approximately 6.76% of all indicator species used in the French index (IBMR), 10.48% in the Portuguese index (IMF) and 12.38% in the Spanish index (BMS). These results show the inadequacy of the trophic indices approach with the HBS conditions and thus the need for the development of an index based on biotic indices approach.