Abstract: Diatoms are an important group of aquatic ecosystems and diatom-based indices are increasingly becoming important tools for the assessment of ecological conditions in lotic systems. Although the studies are very limited about Turkish rivers, diatom indices were used for monitoring rivers in different basins. In the present study, we used OMNIDIA program for estimation of stream quality. Some indices have less sensitive (IDP, WAT, LOBO, GENRE, TID, CEE, PT), intermediate sensitivities (IDSE, DESCY, IPS, DI-CH, SLA, IDAP), the others higher sensitivities (SID, IBD, SHE, EPI-D). Among the investigated diatom communities, only a few taxa indicated alfa-mesosaprobity and polysaprobity. Most of the sites were characterized by a great relative contribution of eutraphent and tolerant ones as well as oligosaprobic and betamesosaprobic diatoms. In general, SID and IBD indices gave the best results. This study suggests that the structure of benthic diatom communities and diatom indices, especially SID, can be applied for monitoring rivers in Southern Turkey.