The paper reveals the problem of measuring reactive oxygen (ROS) and nitrogen (RNS) species' concentrations in plasma treated water Milli-Q. We investigate the features of the FOX method for hydrogen peroxide concentration measurement and the Griess method for nitrite ions concentration spectrophotometric measurement using two different ways of an aqueous solution treatment. In the first case, the electrode (non-conducting high-temperature ceramics) was above the aqueous solution and the discharge was in the gas phase. In the second case, the electrodes were fixed around the perimeter inside the cylindrical chamber filled with water, and working gas (air, argon) was injected into interelectrode space. Varying the duration of exposure (2–10 min) leads to changes in the chemical composition and biological activity of the liquid medium, and this approach is effective for proving of the methods in complex liquids. We found the erosion of the electrodes (stainless steel, duralumin) with the injection of argon and air. The erosion can affect reactions of the methods used, as a result, it makes a contribution to measured concentration. For further applications, it is necessary to consider these features to obtain the correct and reproducible results. When plasma exposure occurs with an electrode that is above the surface of the liquid and does not erode, both methods work in the proper way. But when erosion is present ions of eroded materials (iron, aluminum) contribute to the measurement of hydrogen peroxide concentration using the FOX method. A method with xylenol orange is proposed for taking this feature into account by measuring the concentration of metal ions. In the Griess assay it is possible to obtain strongly erroneous results due to visually similar color and close values of absorbance at the chosen wavelength (525 nm) for both low concentration of nitrites (within linear part of the calibration curve) of nitrites and high concentration (far beyond linear part of the calibration curve). In our research concentration of nitrites does drastically change in the experiment after changing material of the electrodes from stainless steel to duralumin. The Griess assay leads to the formation of a stable fluorescent complex when erosion of the metal electrodes is present.