Water-soluble CuInS₂ ternary quantum dots (QDs) capped by mercaptopropionic acid (MPA) were directly synthesized in aqueous solution, and were then applied to the detection of Cu²⁺ and Cd²⁺ ions. The ternary QDs exhibited obvious photoluminescence (PL) quenching in the presence of Cu²⁺ and marked enhancement in the presence of Cd²⁺ respectively. Other physiological cations such as K⁺, Ca²⁺ Mg²⁺ and Zn²⁺ had no effect on the PL intensity under similar conditions. The detection limits were 0.1 µmol L⁻¹ for Cu²⁺ and 0.19 µmol L⁻¹ for Cd²⁺. The fluorescence quenching of the ternary CuInS₂ QDs by Cu²⁺ could be explained by the reduction of Cu²⁺ to Cu⁺ on the surface of the QDs, whereas the fluorescence enhancement by Cd²⁺ was attributed to activation of surface states. Ternary QDs modified by sufficient Cd²⁺ showed enhanced sensitivity for Cu²⁺ determination compared with unmodified QDs, and a detection limit of 0.037 µmol L⁻¹ was obtained for Cu²⁺. Utilizing the property that Cu²⁺ can be easily removed by addition of iodide, we could eliminate the interference of Cu²⁺ on the Cd²⁺ detection. To the best of our knowledge, this is the first report on the selective detection of Cu²⁺ and Cd²⁺ by quenching and enhancing the fluorescence of the near-infrared CuInS₂ QDs in aqueous solution. This novel method has been successfully applied to the detection of trace Cu²⁺ and Cd²⁺ in real water samples with satisfactory results.