The hydrothermal process assisted by microwaves offers several advantages for processing various materials, including nanoparticles. In this study, we synthesized pure SnO₂ nanoparticles (NPs) and Cu-SnO₂ and Zn-SnO₂ nanocomposites using the hydrothermal synthesis method. Characterization techniques such as X-ray diffraction (XRD), Fourier-transform infrared spectroscopy (FTIR), and scanning electron microscopy (SEM) were employed to confirm the successful synthesis. The XRD analysis revealed that all NPs had a tetragonal rutile crystal structure. FTIR identified a range of functional groups, while SEM images showed that pure SnO₂ NPs formed small clusters. In contrast, the Cu-SnO₂ NPs displayed a semi-spherical shape, and the Zn-SnO₂ NPs exhibited larger spherical structures and interconnected clusters. Energy-dispersive X-ray (EDX) spectroscopy confirmed the presence of tin (Sn), oxygen (O), copper (Cu), and zinc (Zn). The formed nanocomposites were then tested for degradation of indigo caramine and para-nitrophenol. Photocatalytic activity tests demonstrated that Cu-SnO₂ NPs were less effective in degrading toxic indigo carmine dye and para-nitrophenol samples. However, Zn-SnO₂ NPs achieved complete degradation of these compounds within six hours. The findings indicate that the synthesized nanoparticles can effectively degrade the toxicity of harmful substances, such as para-nitrophenol, found in wastewater. This efficacy can be attributed to the efficient separation of electron–hole pairs made possible by surface modification. The unique properties of the prepared nanoparticles makes them valuable in tackling environmental pollution challenges.