In ion chromatography studies, the matrix effect of other inorganic ions present in the sample is a well-known phenomenon. In this work, the behavior of inorganic and organic ions was studied in a system overloaded with ammonium ions. The ammonium ions came from a solution of ammonium hydroxide in various concentrations (0.25-1.25%). In this system, which was significantly overloaded with ammonium ions, the behavior of three ions were tested (lithium, tris, and sodium cations). The measurements were performed at different eluent concentrations (6-17 mM), chromatographic column temperatures (25-40 °C), and injected volumes (15-40 µL). The retention times of sodium and lithium ions increased with increasing amounts of injected ammonium, while tris remained essentially unchanged, indicating that the resolution of these ions can be influenced by varying the concentration of the matrix. The results suggested that the observed effect was due to a combination of the pH change caused by the injected matrix, the dissociation of tris ions, the dissociation of the carbocylic ion-exchange groups of stationary phase, the change in buffer capacity, and the amount of ammonium ion introduced. It has been shown that in a well-designed experiment, the addition of ammonium hydroxide to the sample at concentrations greater than 1% can improve the efficiency of organic and inorganic cation separation. It was found that 8 mM methanesulfonic acid eluent, 30 °C, 1% ammonium hydroxide matrix concentration, and 25 µL injection were optimal for the baseline separation of tris and sodium ions on the high-capacity Dionex CS16 column. These ions could not be separated on this column without the presence of the ammonium matrix.