The goal of this study is to assess the microbial quality of water sources by using conventional culture-dependent microbiological methods and culture-independent molecular-based qPCR application for the monitoring of total bacteria, total coliform, and E. coli as an indicator of fecal contamination. In this experiment, a surface water sample was collected from Gaziantep, Turkey and the detection of microbial load and contamination was performed through gen-specific qPCR, plate count, and MPN quantification techniques. Total bacteria, total coliform, and E. coli levels using qPCR assay were significantly higher than that enumerated by culture-dependent microbiological methods in the water sample. Differences in the water pollution influenced the suitability of molecular method was clarified to the occurring viable but not cultivable (VBNC) bacteria and the measuring of low levels of DNA target by qPCR. The microbial quality of the Gaziantep Alleben water sample predicted by qPCR showed a positive correlation with traditional methods. These results stated that our real-time PCR approach can be suitable to estimate the relative abundances of uncultured and cultured indicator microorganisms affected by the water characteristics. The high level (100%) of resistance observed to clindamycin, erythromycin, penicillin G, tetracycline, and trimethoprim followed cefotaxime (62.5%), ceftazidime (50.0%), streptomycin (50.0%), ciprofloxacin (37.5%), and cefoperazone (25.0%) in a total of 8 strains. The high MAR index (0.33-0.67) of Gr negative strains indicated higher anthropogenic activity such as discharge points of industrial and domestic wastewaters which can contribute to microbiological contamination in surface waters.