This contribution focuses on the interaction of superficial deposits with the marble substrate during the removal by laser radiation. A comparison between cleaning results obtained by the first three harmonic wavelengths of a Q-switched Nd:YAG laser is shown. Experiments were carried out on two sample types. In order to simulate a black encrustation, a model sample was developed based on former studies. In the second case a naturally microbial encrusted marble sample was used. Additionally the temporal ablation development of CaCO3 was investigated by a high speed framing camera. The effects of Nd:YAG laser irradiation at 1064 nm, 532 nm and 355 nm were examined by laser induced breakdown spectroscopy (LIBS), scanning electron microscopy (SEM), energy dispersive x-ray analysis (EDX) and color measurements using the Commission Internationale de l'Eclairge (CIE) Lab color system with respect to the development and the absolute surface color-change. The results show, that the surface color remaining after the removal of the artificial encrustation by the fundamental wavelength, turned from originally white to yellow. It was possible to identify an Iron content located in nanometer sized spheres on the surface to be the source of the yellowing. The third harmonic wavelength removed the encrustation without a discoloration, whereas the second harmonic was not able to remove the crust appropriately. To remove a superficial biogenic encrustation the 2nd and 3rd harmonic were observed to be the most efficient wavelengths, supporting a good result, which could not be achieved by applying the fundamental wavelength.