Freshwater ecosystems are vitally important which supports biological diversity. With this aim, a total of eight biotic and three species diversity indices were used to determine water quality of Kozluoluk Stream in West Anatolia of Turkey. The biotic indices were: Saprobi (SI), Biological Monitoring Working Party (BMWP-O, BMWP-S and BMWP-G), Average Score per Taxon (ASPT), Family Biotic Index (FBI), Belgian Biotic Index (BBI), EPT-Taxa [%], and species diversity indices consisted of: Shannon–Weaver (SWDI), Simpsons (SDI) and Margalef (MDI). Principal component analysis (PCA) was applied to the physicochemical and biotic dataset. Similarities between the sampling stations were clustered by using cluster analysis (CLUS). Pearson-based correlations were used to determine which index is more suitable in determining water quality of the stream. The nine taxonomic groups were found in Kozluoluk Stream consisting of Amphipoda, Oligochaeta, Gastropoda, Ephemeroptera, Plecoptera, Trichoptera, Odonata, Coleoptera and Diptera. The 1st and 2nd stations (90%) were the most similar stations in terms of benthic macroinvertebrate species distribution. The results indicate that the ASPT, BBI, BMWP-O, BMWP-S, BMWP-G and EPT-Taxa [%] are more proper than FBI and SI indices to determine the water quality of Kozluoluk Stream. The water quality along the stream varied from good class in upstream stations, to moderate in downstream stations. This study clearly showed that the specific biotic index according to the ecological characteristics of Turkey should be developed.