•Functional trait-based ecology is poorly developed in species-poor systems.•We show the suitability of two indices of functional diversity in riverine fish.•Indices mostly responded to altitude, physical habitat quality and alien fish biomass.•Taxon richness and other fish indices were poorly related to habitat alterations.•River health misdiagnosis possible if alien fish biomass high and habitat quality good.
Science of the Total Environment – Elsevier
Published: Jun 1, 2018
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