© 2022 by the authors.A molecularly designed imprinting method was combined with a gravimetric nanosensor for the real-time detection Cu(II) ions in aqueous solutions without using expensive laboratory devices. Thus, 1:1 and 2:1 mol-ratio-dependent coordination modes between Cu(II), N-methacyloly-L histidine methyl ester (MAH) functional monomer complexes, and their four-fold and six-fold coordinations were calculated by means of density functional theory molecular modeling. Cu(II)-MIP1 and Cu(II)-MIP2 nanoparticles were synthesized in the size range of 80–100 nm and characterized by SEM, AFM and FTIR. Cu(II)-MIP nanoparticles were then conducted to a quartz crystal microbalance sensor for the real-time detection of Cu(II) ions in aqueous solutions. The effects of initial Cu(II) concentration, selectivity, and imprinting efficiency were investigated for the optimization of the nanosensor. Linearity of 99% was obtained in the Cu(II) ion linear concentration range of 0.15–1.57 µM with high sensitivity. The LOD was obtained as 40.7 nM for Cu(II)-MIP2 nanoparticles. The selectivity and the imprinting efficiency of the QCM nanosensor were obtained significantly in the presence of competitive ion samples (Co(II), Ni(II), Zn(II), and Fe(II)). The results are promising for sensing Cu(II) ions as environmental toxicants in water by combining molecularly designed ion-imprinted nanoparticles and a gravimetric sensor.