Dielectrophoretic assembly and atomic force microscopy modification of reduced graphene oxide J. Appl. Phys. 110, 114515 (2011) Quasi in situ scanning force microscope with an automatic operated reaction chamber Rev. Sci. Instrum. 82, 113709 (2011) Mapping of conservative and dissipative interactions in bimodal atomic force microscopy using open-loop and phase-locked-loop control of the higher eigenmode Appl. Phys. Lett. 99, 074103 (2011) Wideband phase-locked loop circuit with real-time phase correction for frequency modulation atomic force microscopy Rev. Sci. Instrum. 82, 073707 (2011) Additional information on J. Appl. Phys. In ambient conditions, nanometric water layers form on hydrophilic surfaces covering them and significantly changing their properties and characteristics. Here we report the excitation of subharmonics in amplitude modulation atomic force microscopy induced by intermittent water contacts. Our simulations show that there are several regimes of operation depending on whether there is perturbation of water layers. Single period orbitals, where subharmonics are never induced, follow only when the tip is either in permanent contact with the water layers or in pure noncontact where the water layers are never perturbed. When the water layers are perturbed subharmonic excitation increases with decreasing oscillation amplitude. We derive an analytical expression which establishes whether water perturbations compromise harmonic motion and show that the predictions are in agreement with numerical simulations. Empirical validation of our interpretation is provided by the observation of a range of values for apparent height of water layers when subharmonic excitation is predicted.