The water-soluble ammonium (WS-A) in the weathered crust elution-deposited rare earth tailings is adsorbed on the clay mineral surface through weak forces (van der Waals forces and hydrogen bonds), and it is easy to migrate with rainwater, causing serious environmental pollution. Therefore, the study of the elution process of water-soluble ammonium is critical for the remedy of rare earth tailings leached with ammonium. This work aims to investigate the elution process and mechanism of the WS-A from the tailings and determine the optimum elution conditions. Effects of the factors on the removal efficiencies of WS-A were studied under batch and dynamic conditions. Results illustrated that the elution of WS-A is particle size, liquid-solid ratio, pH, ion strength, and temperature dependent, and it was easy to be eluted at weak acid conditions, high liquid-solid ratio, and high temperature from the tailings with small particle size. Moreover, WS-A elution is a fast process controlled by both external and internal diffusion, and a high elution efficiency of 99.98% could be reached under the optimum dynamic conditions. FTIR and XPS showed that nitrogen content was decreased obviously after elution by water, and the concentration gradient diffusion was the main driving force for the elution of WSA absorbed on illite, halloysite, and kaolinite at different interaction sites. This study had great significance in reducing the environmental contamination caused by residual water-soluble ammonium after the in-situ elution of weathered crust elution-deposited rare earth ore.