The UN framework of “Integrated Water Resources Management” recommends countries establish a sustainable management of their water resources, which relies on the availability of proper assessment indexes for the ecological status of surface waters. Such indexes have been developed by many EU countries under the EU Water Framework Directive. Non-EU countries may be interested in adapting such assessment tools. Hence, we describe here a test of three macrophyte-based assessment tools developed in EU countries for use in Armenia. All three indices were tested in a regionally adapted version where local species were entered into reference taxonomic lists, river types were assigned, and matching exercises of the results with benthic macroinvertebrates and physical and chemical parameters of the rivers were performed. The results show that the three tested assessment tools produced similar spatial patterns of ecological status changes, while the adapted version of the MTR index had the highest number of significant correlations with various metrics of macrozoobenthos and hydro-chemical parameters. We conclude that assessment scores for rivers based on macrophytes can be used for rivers of the Caucasus after regional adaptation of the reference macrophyte list. We recommend that the modified MTR index be introduced into the national hydrobiological system of Armenia after some additional adaptations.