Abstract The biological assessment of surface water quality is becoming more important to evaluate the deterioration of aquatic ecosystems and to accomplish environmental sustainability since the implementation of EU Water Framework Directive (WFD). This study as the first attempt was organized to evaluate the ecological status of 17 freshwater bodies in the West of Gaziantep catchment by using diatom metrics. A total of 70 diatom assemblages were identified during the present study. The first two axes of canonical correspondence analysis (CCA) explained 0.962 and 0.945 of diatom assemblages–environment correlations for streams and reservoirs, respectively. According to the CCA, nutrients (e.g., P-PO4 and N-NO3) and metal ions (e.g. Cr, Ni, Pb, and Cu) strongly affected the distribution of diatom assemblages among the water bodies. Among the studied surface waters, Karanlik stream had the highest scores of 3.30, 3.39, and 2.39 due to the TIT–Trophic Index Turkey, TI–Trophic Index, and EPI-D–Eutrophication and/or Pollution Index-Diatom, respectively. The results indicated that this stream had a bad ecological condition when the EPI-D showed a poor condition. The occurrence of pollution-tolerant taxa, associated with high nutrients and electrical conductivity (EC), confirmed the ecological conditions of this stream. On the other hand, Cinarli (TIT = 2.23) and Yamacoba (TIT = 1.96) streams were of good ecological condition and had relatively low EC and nutrients. The presence of pollution-sensitive species in Cinarli and Yamacoba streams (Meridion circulare, Cymbella affinis, Halamphora veneta, and Cymbella excisa) endorsed the ecological status of it. The loading of organic and inorganic nutrients from livestock farming, agricultural land-use, and settlements could impact the water quality of the sampling stations in this catchment. The present study emphasized the importance of the evaluation of ecological integrity based on the biological and chemical characteristics of ecosystems. Diatom indices were used herein reflected efficient results for the separation of the ecological conditions of the sampled stations. Ecological preferences and occurrences of diatom assemblages and the significant positive correlation criterion with P-PO4 confirmed the suitability of TIT for assessing the ecological status of the sampling stations. All of these results suggest that the ecological status of water bodies should be evaluated due to the indices developed in their ecoregions.