Water temperature is one of mainly the seasonal dynamics influencing microbial quality in aquatic ecosystems; however, discerning the interaction betweeen temperature and bacterial diversity is challenging. To address this issue, we characterized the microbial community of surface waters obtained from November month (in 1990 and 2020) with of average 1 °C temperature increase at the Kilis, Türkiye by the 16S rRNA gene sequencing. Bacterial communities indicated high similarities in the relative abundances of dominant taxa (Proteobacteria) for both sampling sites. Our findings highlighted that temperature change favored the duplication of opportunistic thermotolerant bacteria, including total coliform and E.coli which may increase waterborne-disease. This study provides comprehensive information about phylogenetic diversity, quantitatively assessing indicator microorganisms and the physicochemical potential of water quality within two surface waters in Kilis. Our climatic data estimates to be the November average rate of 2.5 °C/increase associated with air temperature of Kilis region for next 30 years. The current study is the first exploration to combine climate change with molecular approaches to predict how bacterial concentrations in aquatic environments may change in future based on long-term air temperature increase for Kilis region.