A novel MnO2@EDTA-Ag nanocoral reef was constructed via a simplified redox reaction followed by EDTA and Ag nanoparticles impregnation to capture hazardous copper (II) from wastewater. A comprehensive characterization of the synthesized materials was conducted. The morphology of MnO2@EDTA-Ag in the form of a nanocoral reef was constructed of two-dimensional nanoplatelets and nanorod-like nanostructures. The optimal adsorption conditions proposed by the Plackett–Burman design (PBD) that would provide a removal % of 99.95 were pH 5.5, a contact time of 32.0 min, a Cu(II) concentration of 11.2 mg L−1, an adsorbent dose of 0.05 g, and a temperature of 40.3 °C. The loading of Ag nanoparticles onto MnO2@EDTA improved the adsorption capability of MnO2@EDTA-Ag. Additionally, the recyclability of MnO2@EDTA-Ag nanocoral reef was maintained at 80% after three adsorption–desorption cycles, and there was no significant change in the XRD analysis before and after the recycling process, implying its stability. It was found that nanocoral reef-assisted EDTA formed a chelation/complexation reaction between COO− groups and C–N bonds of EDTA with Cu(II) ions. In addition, X-ray photoelectron spectroscopy (XPS) and Fourier transform infrared spectroscopy (FTIR) analysis proved the synergistic effect of the electrostatic interaction and chelation/complexation was responsible for the removal mechanism of Cu(II). Also, the results demonstrated no significant variation in MnO2@EDTA-Ag removal efficiency for all the tested real water samples, revealing its efficacy in wastewater treatment. Therefore, the current study suggests that MnO2@EDTA-Ag has substantial potential to be used as a feasible adsorbent for probable hazardous metals remediation.