Assessing the ecological integrity of freshwater ecosystems has become a priority to protect the threatened biodiversity they hold and secure future accessibility to the services they provide. Some of the most widespread applications of biological indicators are fish-based indices. These have mostly mirrored the approach proposed by Karr 30 years ago (Index of Biotic Integrity; IBI), based on the comparison of observed and expected composition and structure of local fish assemblages in the absence of major perturbations, using the so-called reference condition approach. Despite the notable success of the implementation of fish-based indices, most of them overlook non-native species as a source of ecosystem degradation, and evaluations are focused on the physico-chemical condition of freshwater ecosystems and their effects on freshwater biodiversity. Almost 90% of 83 reviewed IBIs did not consider non-native species when defining reference conditions. Most IBIs used non-native species in conjunction with native ones to construct the metrics that conform to the index. The response of the IBI to the effect of non-native species has hardly ever been tested. When developing and evaluating IBIs, attention was mostly directed to ensuring the correct response of the index to physico-chemical parameters, which could otherwise be characterized more effectively using alternative methods. Current application of IBIs entails a misuse of biological indicators by overlooking some types of degradation that cannot be otherwise evaluated by traditional methods. This constrains the capacity to adequately respond to one of the most challenging and common threats to the conservation of freshwater fish diversity.