Mining activities accumulate large quantities of waste in tailing ponds, which results in several environmental impacts. In Cartagena–La Unión mining district (SE Spain), a field experiment was carried out in a tailing pond to evaluate the effect of aided phytostabilization on reducing the bioavailability of zinc (Zn), lead (Pb), copper (Cu) and cadmium (Cd) and enhancing soil quality. Nine native plant species were planted, and pig manure and slurry along with marble waste were used as amendments. After 3 years, the vegetation developed heterogeneously on the pond surface. In order to evaluate the factors affecting this inequality, four areas with different VC and an area without treatment (control area) were sampled. Soil physicochemical properties, total, bioavailable and soluble metals, and metal sequential extraction were determined. Results revealed that pH, organic carbon, calcium carbonate equivalent and total nitrogen increased after the aided phytostabilization, while electrical conductivity, total sulfur and bioavailable metals significantly decreased. In addition, results indicated that differences in VC among sampled areas were mainly owing to differences in pH, EC and concentration of soluble metals, which in turn were modified by the effect of non-restored areas on close restored areas after heavy rains due to a lower elevation of the restored areas compared to the unrestored ones. Therefore, to achieve the most favorable and sustainable long-term results of aided phytostabilization, along with plant species and amendments, micro-topography should be also taken into consideration, which causes different soil characteristics and thus different plant growth and survival.