The use of epilithic diatoms as indicators of river water quality was evaluated in two streams of south Turkey. Diatoms as well as physical and chemical variables were sampled monthly between May, 2002 and April 2003 at six sites that can represent the streams. A total of 110 diatom taxa belonging to 32 genera were found. The most tolerant taxa to organic pollution were Nitzschia palea (Kutzing) W. Smith., Craticula accomoda (Hustedt) D. G. Mann., Gomphonema parvulum (Kutzing) Kutzing, Navicula atomus (Kutzing) Grunow, Navicula cryptocephala Kutzing. These species were dominant at the organically polluted stations. The performance of three types of benthic diatom index was compared ( Swiss Diatom Index (DI-CH), Trophic Index (TI) and Saprobic Index (SI)). The indices were significantly correlated with dissolved oxygen, chloride, biological oxygen demand (BOD(5)), and concentrations of nutrients (NO(3)-N, NO(2)-N, NH(4)-N, and PO(4)-P). DI-CH, TI and SI had high correlations with the physicochemical variables but DI-CH and TI were more reliable than the SI. We concluded that in these rivers, DI-CH and TI could be more useful than SI. Based on the significant correlation with nutrients and organic pollution variables this study suggests that SI, TI and DI-CH are integrating the effects of organic pollution.