Quantum dots have been considered to be promising candidates for bioapplications because of their high sensitivity, rapid response, and reliability. The synthesis of high-quality quantum dots that can be dissolved in water and other biological media is a crucial step toward their further application in biology. Starting with a one-pot reaction and the successive ionic layer adsorption and reaction (SILAR) method, we produced the CdSe/ZnS core/shell structure. Through a ligand-exchange mechanism, we coated the as-made CdSe/ZnS structure with 3-mercaptopropionic acid (MPA) or mercaptosuccinic acid (MSA). Various techniques, including photoluminescence (PL), ultraviolet-visible (UV-Vis) spectroscopy, transmission electron microscopy (TEM), X-ray diffraction (XRD), and Fourier transform infrared (FTIR) spectroscopy, were utilized to characterize the ligand-coated CdSe/ZnS structure. The results show enhanced luminescence intensity, CdSe surface passivation by ZnS, and successful coating with MPA and MSA. The stability of quantum dots in solutions with different pH values was investigated by performing zeta potential measurements. The results revealed that the quantum dots shifted from displaying hydrophobic to hydrophilic behavior and could be connected with bioagents.