In this study, ion-exclusion/cation-exchange chromatography (IEC/CEC) using dual-ion-exchange groups (carboxy and sulfo groups) for the simultaneous determination of anions (SO42−, Cl−, NO3−, and HPO42−) and cations (Na+, NH4+, K+, Mg2+, and Ca2+) was developed. By using the combination of dual-ion-exchange groups, simultaneous separation of inorganic ions with HPO42− was achieved that was impossible by the conventional IEC/CEC based on the single-ion-exchange group (carboxy group). This method was applied to the monitoring of inorganic ionic nutrients in fertilizer solution samples in hydroponic culture. As a result, a higher peak resolution of inorganic anions and cations with phosphate ion using IEC/CEC with dual-ion-exchange groups was achieved in the absence of matrix effects. In addition, the developed method helps to understand the behavior of ionic nutrients in fertilizer solution during hydroponic cultivation and is potentially useful for the individual fertilization of ionic nutrients.