Semiconductor quantum dots are considered very promising candidates for bio-imaging and diagnosis applications because of their tunable optical properties and good optical stability in aqueous phase. Any practical application of these materials will rely on the viability of their simple and direct synthesis in aqueous phase with no need for toxic and unstable organic media. The optical properties of CdSe quantum dots and CuS nanoparticles are desirable in bio-imaging and cell sorting applications because of their tunable photoluminescence at the visible range. The present work addresses the synthesis of CdSe quantum dots and CuS nanoparticles via an optimized, simple and scalable aqueous processing route at low temperatures. The tunability of the optical properties was achieved by a suitable control of the citrate/Cd mole ratio, temperature of synthesis (20-90°C) and reaction time (0-1 hour). In the case of CuS, the strong plasmonic absorption offers the opportunity to investigate this material as a photothermal coupling agent for photothermal therapy. The intensity of the plasmonic absorption was enhanced by selecting an appropriate sulfide precursor (Na2S, Thioglycolic acid), temperature of synthesis (90-120°C) and reaction time. Nanocrystals were characterized by x-ray diffraction, UV-VIS, photoluminescence (PL) spectroscopy techniques and electron microscopy. The effects of the synthesis conditions on the crystal size and the corresponding functional properties of synthesized quantum dots are presented and discussed.