We have developed a simple and homogeneous fluorescence assay, comprised of 3-mercaptopropionic acid (MPA) and DNA-Cu/Ag nanoclusters (NCs) in aqueous solution, for the detection of Cu(2+) ions. The fluorescence of the DNA-Cu/Ag NCs was quenched by MPA, which was recovered in the presence of Cu(2+) ions. This MPA-induced fluorescence quenching arises through changes in the DNA conformation that occur after interactions between MPA and the Cu/Ag clusters. The MPA-induced fluorescence quenching displayed typical characteristics in Stern-Volmer plots; it followed a static quenching mechanism. The presence of Cu(2+) ions resulted in the oxidation of MPA to form a disulfide compound, leading to recovery of the fluorescence of the DNA-Cu/Ag NCs. The fluorescence of the DNA-Cu/Ag NCs in the presence of MPA increased upon increasing the concentration of Cu(2+) ions over the range from 5 to 200 nM. The DNA-Cu/Ag NC probe provided the limit of detection (at a signal-to-noise ratio of 3) for Cu(2+) ions of 2.7 nM, with high selectivity (by at least 2300-fold over other tested metal ions). We validated the practicality of using this probe for the detection of Cu(2+) ions in environmental samples through analyses of Montana soil and pond water samples.