Adsorbable organic halogen (AOX) represents the total amount of halogenated organics that can be adsorbed on activated carbon (AC) from samples. Measuring AOX is crucial for assessing water quality, and any erroneous estimation of AOX risks misleading decision-makers. This study demonstrated two overlooked factors that may introduce biases to AOX measurement. The first one relates to impurities in the gas transfer tubes of AOX combustion system and in the pressurized gas of AOX separation system, which resulted in significant fluctuations and high blank values (8.5–118.0 μg-Cl/L). The solutions of above issues are to warming up the combustor for several runs and replacing the pressurized air with argon gas in the separator, which could drop the blank AOX values to 9.1–10.0 μg-Cl/L. The second one involves coexisting chloride ion (Cl−) during AOX analysis, which interfered with AOX measurements (T. test, p < 0.05) even at low concentration levels (e.g., 10 mg/L Cl− in samples with 100 μg-Cl/L p-chlorophenol). Results show that AC captured 0.02–0.11 % of Cl−, resulting in 17.7–24.5 μg-Cl/L AOX responses in control samples containing 15–130 mg/L Cl− only. Furthermore, a significant mass imbalance of Cl− (3.58–8.39 %) during analysis process suggests a potential impact of residual Cl− on subsequent samples. By comparing synthetic and actual waters, samples with low dissolved organic carbon (DOC) were more susceptible to interference from Cl− on AOX measurement than those with high DOC. These findings underscore the pressing need to optimize existing AOX methods or develop alternative analytical methods to ensure accurate water quality assessment.