Loess is widely distributed in Northwestern China and serves as the preferred engineering construction material for anti-fouling barriers. Heavy metal contamination in soil presents significant challenges to the engineering safety of vulnerable loess structures. Hence, there is an urgent need to investigate the impact of heavy metal ions on their percolation performance. In order to investigate the effectiveness of microbially induced carbonate precipitation (MICP) using Sporosarcina pasturii (CGMCC1.3687) bacteria in reducing internal seepage erosion, a saturated permeability test was conducted on reshaped loess under constant water head saturation conditions. The response of loess to deionized water (DW) and ZnCl2 solution seepages was analyzed by monitoring changes in cation concentration over time, measuring Zeta potential, and using scanning electron microscopy (SEM). The results indicate that the hydrolysis of Zn2+ creates an acidic environment, leading to the dissolution of carbonate minerals in the loess, which enhances its permeability. The adsorption of Zn2+ ions and the resulting diffusion double-layer (DDL) effect reduce the thickness of the diffusion layer and increase the number of free water channels. Additionally, the permeability of loess exposed to ZnCl2 solution seepage significantly increased by 554.5% compared to loess exposed to deionized water (DW) seepage. Following the seepage of ZnCl2 solutions, changes in micropore area ratio were observed, decreasing by 48.80%, while mesopore areas increased by 23.9%. MICP treatment helps reduce erosion and volume shrinkage in contaminated loess. Carbonate precipitation enhances the erosion resistance of contaminated loess by absorbing or coating fine particles and creating bridging connections with coarse particles. These research results offer new perspectives on enhancing the seepage properties of saturated loess in the presence of heavy metal erosion and the geochemical mechanisms involved.