Water soluble Mercaptoacetic acid (MAA)-capped CdS/ZnS core-shell quantum dots (QDs) was synthesised and characterised by using the UV-Visible absorption spectroscopy, Fluorescence spectroscopy, Fourier Transform Infrared Spectroscopy (FT-IR) and Transmission Electron Microscopy (TEM). These functionalised QDs are used as fluorescence probe for the determination of Hg(II) ions, based on the fluorescence quenching of QDs. A high optical selectivity and sensitivity toward Hg(II) ions was obtained at pH 7.4 of Tris–HCl buffer with a QDs concentration of 12.0?mgL?1. Under optimum conditions, the fluorescence intensity of CdS/ZnS QDs was linearly proportional to mercury ions concentration in the range 0.025?×?10?7 to 2.8?×?10?7?M with a detection limit of 2.2?×?10?9?M. The effect of common foreign ions on the fluorescence of the QDs was examined which confirmed high selectivity of this material towards Hg(II) ions. Measurements of real samples also give satisfactory results which were in good agreement with those obtained using Atomic Absorption Spectroscopy. Therefore, these QDs are not only sensitive and of low cost, but also can be reliable for practical applications.