Selecting the appropriate counter-ion for an ion-exchange membrane depends on the research objective. Generally, it is important to use counter-ions having the lowest affinity for the ion-exchange membrane (i.e., easily desorbed); thereby, allowing nutrient ions in the soil solution to be readily adsorbed. Commonly, H⁺ and OH^- are used as counter-ions for cation and anion-exchange membranes, respectively. However, depending on the soil type, the H⁺ form may be inappropriate. For example, in calcareous soils the H⁺ reacts with abundant CaCO₃ and liberates Ca²⁺. This large quantity of free Ca²⁺ interferes with NH₄⁺ and K⁺ adsorption and will affect NH₄⁺ and K⁺ supply rate measurements if the ion-exchange membrane is left in soil for a long period of time. Furthermore, the addition of H+ and OH- may introduce undesirable rhizosphere effects (i.e., pH), which will affect nutrient availability.

The cation and anion-exchange PRS™-probes use Na⁺ and HCO₃^- as the counter-ion, respectively. Using Na⁺ as the counter-ion is more desirable because its relative affinity is the next lowest in the order to H⁺, while avoiding any undesirable rhizosphere effects (i.e., reduced pH). Similarly, HCO₃^- is advantageous due to its relatively low affinity, but also the desorbed HCO₃^- bio-mimics the HCO₃^- produced in the rhizosphere during plant root and microbial respiration. In addition, the HCO₃^- is not conserved in the solution, thereby helping to overcome the complementary anion effect, which tends to decrease adsorption of the target ion. Saturating the ion-exchange membrane with the same counter-ion ensures consistent ion-exchange chemistry across the entire PRS™-probes’ ion-exchange membrane, thereby, increasing the measurement precision among treatments.