Nanotechnology offers a great opportunity for efficient removal of pollutants and pathogenic microorganisms in water. Copper nanoparticles were synthesized using a polysaccharide bioflocculant and its flocculation, removal efficiency, and antimicrobial properties were evaluated. The synthesized nanoparticles were characterized using thermogravimetry, UV-Visible spectroscopy, Fourier-transform infrared spectroscopy (FT-IR), powder X-ray diffraction, scanning electron microscope (SEM), and transmission electron microscope (TEM). The highest flocculation activity (FA) was achieved with the lowest concentration of copper nanoparticles (0.2 mg/mL) with 96% (FA) and the least flocculation activity was 80% at 1 mg/mL. The copper nanoparticles (CuNPs) work well without the addition of the cation as the flocculation activity was 96% and worked best at weak acidic, neutral, and alkaline pH with the optimal FA of 96% at pH 7. Furthermore, the nanoparticles were found to be thermostable with 91% FA at 100 °C. The synthesized copper nanoparticles are also high in removal efficiency of staining dyes, such as safranin (92%), carbol fuchsine (94%), malachite green (97%), and methylene blue (85%). The high removal efficiency of nutrients such as phosphate and total nitrogen in both domestic wastewater and Mzingazi river water was observed. In comparison to ciprofloxacin, CuNPs revealed some remarkable properties as they are able to kill both the Gram-positive and Gram-negative microorganisms.