In the last two decades, quantum dots (QDs) have demonstrated great potential for biophotonics applications such as optical imaging and analytes sensing. For these purposes, cadmium-based (Cd-based) QDs are most commonly used because of their excellent optical properties, while cadmium-free (Cd-free) QDs are attracting increasing attention due to the low toxicity of their components. Generally, for use in biological fluids, QDs are either prepared using the aqueous synthesis method or the hot colloidal synthesis method followed by a phase transfer process. This thesis studies the preparation of water-dispersible Cd-based and Cd-free QD by using these two methods and explores their potential for biophotonics applications. First, this thesis presents a facile aqueous synthesis method for preparing the biofunctionalized Cd-based QDs. The CdTe QD nanocrystals were fabricated in a microfluidic chip by using protein molecules as coordination ligands. Compared to the conventional bench-top method, the microfluidic synthesis approach produced the CdTe QDs with enhanced stability and improved biofunctionalization efficiency. Another method of preparing the aqueous QDs, phase transfer of the QDs synthesized in organic solvents, was also examined. Hydrophilic ligands with different chain lengths and functional groups were applied to render the QDs water-dispersible by using the ligand exchange method. Each set of QDs capped with specific surface ligands displayed strengths and limitations in certain aspects of their physicochemical properties, and induced different cellular responses. To mitigate toxicity concerns in biophotonics applications, Zn-Cu-In-S QDs, which are quaternary and Cd-free QDs, were prepared using a facile aqueous synthesis method. The composition effect on their optical properties is demonstrated and correlated with the Abstract 5 evolution of their structure and energy band gap. Using the same strategy of composition control, Zn-Ag-In-S QDs with different emission wavelengths were synthesized in the organic phase and then transferred into the aqueous phase via the encapsulation method. The resulting water-dispersible ZAIS QDs exhibited bright photoluminescence and long fluorescence lifetime and were applied in temporally multiplexed imaging of cells. Finally, ZnO QDs, a type of Cd-free QDs made from wide-band-gap oxides, were prepared using the sol-gel method. Their optical properties were modified via chemical doping and photodoping techniques. Their redox-sensitive photoluminescence and plasmonic properties make them promising candidates for biosensing applications. In summary, this thesis covers the manipulation of optical properties, surface chemistry and biocompatibility of Cd-based and Cd-free QDs using versatile strategies in synthesis and surface modification processes, and demonstrates the potential of using these QDs in biophotonics applications.