Carbonates, in the form of natural or artificially added calcite, are known to increase the buffering capacity of clayey soils. Consequently, they enhance soil’s ability to retain contaminants. However, carbonate-rich soils demonstrate resistance to contaminant removal in electrokinetic remediation processes. Previous research has mainly focused on the solubility of carbonates and the precipitation of heavy metal-carbonate compounds, but the effect of carbonates on the surface potential of clayey soils in alkaline and acidic environments has received limited attention. This paper aims to explore the impact of carbonate on the surface potential variations of kaolinite.To achieve this, a series of zeta potential experiments were conducted on kaolinite samples containing 2% natural carbonate and on de-carbonated kaolinite. Additionally, X-ray diffraction (XRD) and SEM experiments were performed to examine the microstructural aspects of the study. The findings reveal that carbonate significantly influences the zeta potential variations of kaolinite in acidic and alkaline environments. The presence of carbonate creates resistance to changes in kaolinite’s zeta potential, resulting in a specific region on the zeta potential curve where the soil exhibits relatively constant zeta potential. The experimental results suggest that the zeta potential pattern of carbonated kaolinite theoretically substantiates the role of carbonate in the interaction process of heavy metals with carbonated clay.