Nutrient availability in hydroponic solutions must be accurately monitored to maintain crop productivity; however, few cost-effective, accurate, real-time, and long-term monitoring technologies have been developed. In this study, we describe the development and application of cation-/anion-exchange chromatography with a neutral eluent (20 mmol/L sodium formate, pH 7.87) for the simultaneous separation (within 50 min) of ionic nutrients, including K+, NH4+, NO2–, NO3–, and phosphate ion, in a hydroponic fertiliser solution. Using the neutral eluent avoided degradation of the separation column during precipitation of metal ion species, such as hydroxides, with an alkaline eluent and oxidation of NO2– to NO3– with an acidic eluent. The suitability of the current method for monitoring ionic components in a hydroponic fertiliser solution was confirmed. Based on our data, we propose a controlled fertiliser strategy to optimise fertiliser consumption and reduce the chemical load of drained fertiliser solutions.