A high throughput nanozyme-based catalytic system was developed for eco-friendly nanozyme-mediated biodegradation of organic dye, methylene blue, in real water media. The above-mentioned nanozymes were synthesized and then characterized for their morphology, composition, and size by Transmission Electron Microscopy (TEM), elemental mapping, and Dynamic Light Scattering (DLS) analysis, in order. The nanozymatic properties of the as-prepared nanomaterials were evaluated by standard enzyme activity assay, revealing high peroxidase-like performances for the as-prepared nanozymes. Therefore, for more precise reporting of the peroxidase-like performances of the nanozymes, the kinetics behavior of the as-prepared nanozymes was evaluated by the standard Lineweaver-Burk method, revealing a Vmax as high as 0.263 µM sec-1 and a Km as low as 0.03 mM, revealing high catalytic efficiency and affinity of the as-prepared nanozymes. Hence, the as-prepared nanozymes were utilized for the degradation of organic dye in real water utilizing methylene blue as a model dye. The factors affecting the dye degradation including pH, degradation time, ionic strength, nanozyme amount, etc. were optimized utilizing the one-factor-at-a-time optimization method. At optimal experimental conditions, the as-prepared nanozymes can degrade about 99.0% of the organic dye within a degradation time as low as 7 min. The developed method was finally employed for the nanozyme-mediated degradation of methylene blue from real water media such as pool water, mineral water, river water, and tap water samples. The results of this study revealed an excellent biodegradation yield of over 94.3%-99.0% for the different real samples, proving the suitability of the developed method for dye degradation in real media.