In this study, metallic iron nanoparticles (Fe NPs) and metallic copper nanoparticles (Cu NPs) were prepared, characterized, and used in the removal of methyl orange (MO) dye. The experiments investigated first the UV–Vis spectra of dye molecules in three types of solvents (water, water-ethanol, and water-dimethyl sulfoxide). The removal of MO was then conducted under various experimental conditions to investigate the effects of solvent type, nanoparticles dosage, salinity of the solutions, temperature, and shaking time. The highest extent of MO removal was achieved in water solutions. Under all experimental conditions, Fe NPs showed higher efficiency than Cu NPs in MO removal. Moreover, heterogeneous Fenton process led to smaller MO removal when compared with the direct use of the nanoparticles, for both water and water-ethanol solutions. From a kinetic perspective, the dye removal process was much faster in water than in water-ethanol mixtures, and the data followed pseudo-second order rate equation.