The interactions between hydrophobic or semihydrophobic gold and silver nanoparticles (NPs) and a dimyristoylphosphatidylcholine (DMPC) bilayer as a model cell membrane in two ionic solutions result in the structural reorganization within the bilayer manifested as locally increased nanomechanical compaction in the vicinity of NP clusters as well as changed overall thermotropic properties. The effects of NP surface charge and hydrophobicity were examined using AFM imaging, force spectroscopy and IR spectroscopy. The NP clustering occurred during hydration process of dry films containing both the DMPC molecules and the NPs by the mechanism in which the number of bilayer deformations was reduced by NP clustering. The force spectroscopy showed increased bilayer density around (semi)hydrophobic NP clusters and thus locally increased lateral compaction of the bilayer. The strengthening effect was observed for both the silver and the gold NPs in a high ionic strength solution such as seawater, while it was absent under physiological conditions. The local lipid rearrangement induces the long-range lipid reorganization resulting in the bilayer phase transition shifting toward lower or higher temperatures depending on the solution ionic strength (at the most by -1.0 °C in phosphate buffered saline and at the most by +0.5 °C in seawater).