Many cost-effective and environmentally friendly strategies are applied to improve soil fertility, reduce soil pollution, and reduce the human health risks of consuming metal-contaminated vegetables. We evaluated the effects of three soil amendments, biochar, slag and ferrous manganese ore (FMO), at application rates of 3% and 6%, on the bioavailability of heavy metals in a contaminated soil, their bioaccumulation, and antioxidant enzyme activities in water spinach (Ipomoea aquatica) plants. We also measured a range of soil physicochemical and biological properties, as well as plant biomass. Application of biochar at 6% was the most effective treatment for improving the fresh biomass of plants, with an increase of 32.31% in the roots and 47.98% in the shoots relative to the unamended soil. Compared with slag and FMO, biochar was most effective in improving soil physicochemical and biological properties. All amendments significantly reduced the bioavailability of lead and cadmium. We observed significantly positive correlations among bio-concentration factor, translocation factor and bioaccumulation coefficient. Correlation analysis also demonstrated that bulk density was positively correlated with soil available water content, but negatively correlated with soil organic matter, total porosity and hydraulic conductivity. Soil macro- and micronutrients were found to have a positive correlation with soil physical, chemical and biological properties. In conclusion, biochar, slag and FMO significantly affected the physical, chemical and biological properties of soil, and metal bioavailability and fertility status, safeguarding soil health and ensuring the healthy growth of the plants.