Ion-selective electrodes (ISEs) are among the most successful electrochemical sensors used in various applications because of their ability to measure electrolyte concentrations in liquids easily. It is common practice to suppress ion fluxes through the ion-sensitive membranes in ISEs because such fluxes worsen the lower limit of detection. In this study, we propose a method to detect interfering ions using this ion flux phenomenon. As a proof of principle, a flow-type Cl-ISE based on an ion exchange membrane loaded with the target ion chloride was used to acquire transient potential profiles during standstill after the introduction of liquids containing various ion species. When the target ion of the ion-sensitive membrane was measured, there was almost no change in potential over time. In contrast, when hydrophilic interfering ions were measured, the potential gradually decreased, and when hydrophobic interfering ions were measured, the potential gradually increased. The direction and intensity of these changes over time depended on the ion species and concentrations. The main reason for these potential changes is presumed to be the change in the local ionic composition of the sample near the sensing membrane due to ion exchange between the sample and membrane. This phenomenon could not be observed in a hydrophobic ion exchanger membrane doped with a quaternary ammonium salt and was characteristically observable using hydrophilic ion exchange membranes with a high charge density and a high ion diffusion rate. Finally, using a high-throughput flow-type system, we demonstrated the detection of interfering ions in solutions containing multiple ion species by using the ion flux phenomenon.