In this study, we attempted to calculate the Natural Background Level (NBL) for 19 selected chemical compounds in the Urmia aquifer, northwestern Iran. In this study, combined methods including pre-selection and statistical methods for determining NBL have been used. In the pre-selection method, the concentration of nitrate (NO3 ≥ 19.97 ppm) and chloride (Cl ≥ 200 ppm) were used as the main criteria to identify and eliminate samples affected by human activities. The selected concentration of nitrate is determined using the comparison of the results of various statistical and graphical evaluations including Quantile-Quantile plot (Q-Q plot), Box & Whisker plot (BW), Box & Whisker plot Iterative (BWI), Grubbs test, Mean and standard deviation (mean ± 2σ) (MSD), and median absolute deviation (MAD). After identifying the final data set, the NBL of the selected chemical compounds was calculated by two techniques including the Iterative 2σ technique (2σ) and calculated distribution function (CDF). Due to higher concentration relative to the reference values (REF), this study has focused on the calculation of NBL of SO4, F, As, Fe and Mn. Results showed that the upper limit of NBL calculated for these variables is about 125 ppm, 1 ppm, 8.5 ppb, 570 ppb, 80 ppb, respectively. Given that no study has been conducted to determine the NBL of chemical compounds in groundwater in Iran, the results of this study can be a roadmap for decision-makers and researchers to better manage this aquifer and other water resources in this country with limited freshwater resources.