In this study, a sensing device employing a gold-coated quartz tuning fork (QTF) modified with a self-assembled monolayer (SAM) of L-cysteine was evaluated for the sensitive detection of Cu2+ ions in aqueous solutions. Three copper (II) salts, CuSO4, CuCl2, and Cu(NO3)2, at four different concentrations (10−12, 10−10, 10−8, and 10−6 M) in small (100 μL) water sample amounts were each used as analytes to investigate the influence of their counterions in the detection of the Cu2+ ions. It was found that, among the counterions, the sulfate anion had the largest effect upon the detection of Cu2+ in water, in the following order: SO42− > Cl− > NO3−. The lower limit of detection of the Cu2+ ions detected was in the 10−12 M range. The frequency shifts measured with the QTFs relative to deionized water were inversely proportional to the concentration/mass of the analytes. Density functional theory calculations were conducted to understand the effect of the counterions on the respective electronic interaction energies for the apparent host–guest binding of the analytes with L-cysteine and with gold surface-bound L-cysteine molecules. Gas phase (both with and uncorrected BSSE) and solution phase interaction energies (ΔIE) calculated at the B3LYP/LANL2DZ and ωB97XD levels of theory showed that the stability for the complexes were in the following order: [L-cysteine]⊃[CuSO4] > [L-cysteine]⊃[CuCl2] > [L-cysteine]⊃[Cu(NO3)2], which supports our experimental findings, as they were in the same order as the experimentally observed order for the copper salts tested: CuSO4 > CuCl2 > Cu(NO3)2.