Nanotechnology addresses numerous environmental problems such as wastewater treatment. Ground water, surface water and wastewater that is contaminated by toxic organic, inorganic solutes and pathogenic microorganisms can now be treated through the application of nanotechnology. The study reports iron@copper (Fe@Cu) nanoparticles, iron nanoparticles (FeNPs) and copper nanoparticles (CuNPs) synthesized using a bioflocculant in a green approach technique. Characterization of the as-synthesized materials was achieved using analytical techniques such as Fourier transform-Infrared spectroscopy (FT-IR), Thermogravimetric analysis (TGA), Scanning Electron Microscope (SEM), Transmission Electron Microscopy (TEM), UV-Vis spectroscopy (UV-Vis) and X-ray diffraction (XRD). The presence of hydroxyl (−OH) and amine (−NH2) groups was shown by FT-IR spectroscopy studies and the as-synthesized material was shown to be thermostable. Elements such as oxygen, carbon, iron and copper were found to be abundant in Wt%. Absorption peaks were found between 200 and 390 nm wavelength and diffraction peaks at 2θ −29°, 33° and 35° for FeNPs, CuNPs and Fe@Cu, respectively. In their application, the effect of various parameters on the flocculation activity were evaluated. Both the CuNPs and (Fe@Cu) nanoparticles have shown the best flocculation activity at a concentration of 0.2 mg/mL with over 90% activity, while the dosage size with a concentration of 0.4 mg/mL was optimal for FeNPs. The FeNPs were found to be cation dependent, while CuNPs and Fe@Cu nanoparticles flocculate in the absence of a cation and flocculate both in acidic and alkaline pH. All the synthesized nanoparticles are thermostable and maintain flocculation activity above 80% at 100 °C. Both the Fe@Cu and CuNPs were found to be effective in removing dyes with the removal efficiency above 89% and were found to be effective in removal of chemical oxygen demand (COD) and biochemical oxygen demand (BOD) in Mzingazi river water and coal mine wastewater with over 80% removal efficiency. Moreover, the synthesized nanoparticles showed some remarkable antimicrobial properties when evaluated against Gram-positive and Gram-negative bacteria. The as-synthesized material was found to be safe to use at low concentration when verified against human embryonic cells (HEK293) and breast cancer cells (MCF7) and biodegradable.