The biological assessment of inland waters using ecological criteria is becoming more important due to the need to evaluate and monitor aquatic environments that are under heavy environmental stress. Turkey has been trying to develop a model to understand its inland waters in terms of the European Water Framework Directive's (WFD) European fish index (EFI). The EFI is derived from assessment of five biological elements. The EFI is inappropriate for the conditions in Turkish inland waters; thus, the present study developed a fish-based index of biotic integrity for Turkey (FIBI-TR) as a suggestion. To assess the adequacy of the FIBI-TR, this study gathers field data in two selected basins in 2013 and 2014 according to WFD criteria for biological elements and physicochemical parameters, simultaneously. The FIBI-TR was then compared to the scores derived from the WFD score, which was a cumulative score for all related biological elements, and with other frequently used indices such as the Water Pollution Control Directive and trophic state index. Based on these data, the FIBI-TR seems to be congruent with cumulative WFD scores. However, the FIBI-TR does not agree with other indices based on physicochemical parameters. Detailed research is needed if WFD is to be adapted for Turkey through FIBI-TR.