In this work, the scratch and indentation properties of the outer and inner (nacre) layers of green mussel shells under dry and water-soaked conditions were investigated. In micro-scratch tests with increasing normal load, it was found that the scratch hardness of the inner and outer shell surfaces tended to decrease rapidly at lower loads as compared to the changes in hardness at higher loads. The readings varied in the ranges of 1.5–2.4 and 0.8–2.0 GPa for inner and outer surfaces, respectively. In nano-indentation tests, the responses of inner nacre were not affected by prior soaking as much as those of the outer shell surfaces. The outer shell surfaces showed a significant drop in nano-hardness from 4.5 to 2.8 GPa, while the Young's modulus increased from 62 to 84 GPa after soaking. However, the average nano-hardness and modulus of elasticity of nacreous inner layer only varied slightly in the range of 4.5–4.1 and 64–61 GPa, respectively. In addition, Vickers hardness readings showed that there was a detectable steady increase in micro-hardness of nacre as soaking time increased, although the differences were small. The reverse trend was observed for the outer layer. Analysis of the shells using Fourier transform infrared (FTIR) in reflectance mode gave strong evidence of the presence of sulphated saccharides, polyglycine and hydro-complex in the organic phase of the shell. Their interaction with calcium carbonate of the shell during scratch and indentation tests could be affected with the permeation of water due to soaking of shells.