Polychlorinated dibenzodioxins (PCDD) and Polychlorinated dibenzofurans (PCDF) are two groups of toxic substances that belong to the group of persistent organic substances (POP) that are receivedconsiderable attention and various analytical methods for determination of PCDD/Fs have been developed. Analytical method using gas chromatography and high-resolution mass spectrometry (GCHRMS) system with high resolution and excellent sensitivity has long been considered as a standard method for dioxins analysis. Simultaneously, the triple quadrupole gas chromatography-mass spectrometry system (GC-MS/MS) with sensitivity equal to GC-HRMS and reduced operating and maintenance costs, is being actively researched and developed for dioxin analysis as an alternative to GC-HRMS. This paper reports the operating conditions and the results of dioxin analysis in the water sample on the GC-MS/MS system, and direct comparison with the results obtained from GC-HRMS. Both equipments demonstrated a good consistency in sensitivity and results of concentrations in water samples, but the GC-MS/MS system showed superior Signal-to-Noise signal compared to GC-HRMS. GC-MS/MS showed good repeatability and reproducibility and met the requirements of dioxin analysis method, comparable to GC-HRMS. With the advantage of low initial cost and much lower operating and maintenance costs than GC-HRMS, GC-MS/MS proved to be a potential method for analyzing dioxins in water samples