In the framework of developing a portable label-free sensor for multi arrayed detection of heavy metals in drinking water, we present a mechanical resonator-based copper ions sensor, which uses a recently synthesized peptide Cysteine–Glycine–Glycine–Histidine (CGGH) and the l-Cysteine (Cys) peptide. In this work we combine the selectivity of two different functionalization layers with the very high distributed mass to frequency sensitivity of our bulk mechanical resonator. The resonator is a polysilicon disk which shows a Q-factor of 6500 in air at 65.3MHz, while the two capturing chelating peptides CGGH and Cys have been immobilized via thiol groups on its surface. Insight on the interaction between the novel CGGH peptide and copper ions is obtained, demonstrating a 4.8 times larger binding efficiency than expected compared to a precedent model. After demonstrating the ability of the functionalized devices to detect a concentration of 10μM of copper in water, we regenerate the surface by removing the copper ions from the functionalization layer using EDTA.