Nanodiamonds coated with dopamine-squaramide compounds have been prepared by a calcination/esterification synthetic process, which improves the efficiency of this carbonaceous material with respect to non-functionalized nanodiamonds. The modified nanodiamonds show excellent selective coordination of Ag+ and Au3+ cations in a Cd2+, Co2+, Cr3+, Cu2+, Pb2+, and Zn2+ mixture in water. The coordination capacity of the carbonyl squaramide groups with the silver and gold cation is based on purely electrostatic cation-dipole interactions. Overall, it is demonstrated that the conjunction between the nanodiamonds and the organic receptor improves the selectivity of the material toward noble cations.