Functional nanocomposites with biopolymers and zinc oxide (ZnO) nanoparticles is an emerging application of photocatalysis in antifouling coatings. The reduced chemical stability of ZnO in the acidic media in which chitosan is soluble affects the performance of chitosan nanocomposites in antifouling applications. In this study, a thin shell of amorphous tin dioxide (SnOx) was grown on the surface of ZnO to form ZnO–SnOx core–shell nanoparticles that improved the chemical stability of the photocatalyst nanoparticles, as examined at pH 3 and 6. The photocatalytic activity of ZnO–SnOx in the degradation of methylene blue (MB) dye under visible light showed a higher efficiency than that of ZnO nanoparticles due to the passivation of electronic defects. Chitosan-based antifouling coatings with varying percentages of ZnO or ZnO–SnOx nanoparticles, with or without the glutaraldehyde (GA) crosslinking of chitosan, were developed and studied. The incorporation of photocatalysts into the chitosan matrix enhanced the thermal stability of the coatings. Through a mesocosm study using running natural seawater, it was found that chitosan/ZnO–SnOx/GA coatings enabled better inhibition of bacterial growth compared to chitosan coatings alone. This study demonstrates the antifouling potential of chitosan nanocomposite coatings containing core–shell nanoparticles as an effective solution for the prevention of biofouling.