The study delves into the Zaalklapspruit valley-bottom wetland in South Africa, a site designed through ecological engineering and currently impacted by acid mine drainage due to an upstream defunct coal mine. The research conducted in 2022, aimed to uncover the dynamics of contaminant dispersal within such a wetland setting, focusing on the origins, routes, and ultimate recipients of various metals and sulfur compounds. Analysis revealed that the bottom sediment is rich in organic material, with pH levels observed between 6.05 and 6.59, and exhibited notably low oxidation-reduction potentials, reaching down to −219.67 mV at sample point S3. Notably, Manganese displayed the highest adsorption rates, whereas Iron was predominantly absorbed by the roots of Typha capensis and the algae Klebsormidium acidophilum. The wetland's macrophyte rhizospheres hosted a rich array of microbiota, including families like Helicobacteraceae and Hydrogenophilaceae, which are crucial in metal and sulfur processing. This investigation sheds light on the intricate biogeochemical processes taking place involving the wetland's sediment, macrophyte root systems, periphyton, and microbial populations, underscoring the potential of ecologically engineered wetlands in the remediation of waters affected by acid mine drainage.