We report the physical and photophysical properties of CdSe quantum dots capped with three different thiol compounds (thioglycolic acid, 3-mercaptopropionic acid, mercaptosuccinic acid) synthesized through a hydrothermal protocol. We calculated the true molecular weight and molar absorption coefficient of QDs from their diameter (not from any empirical relation) which are in the range 3.5 – 5.9 nm. The aqueous synthesis method ensures the insertion of the sulfur atoms of thiol ligands in the crystal CdSe cubic lattice, producing hexagonal crystal unit defects at the surface of the QDs. The QDs steady-state emission spectra were analyzed in terms of Gaussian components, in correlation with the time-resolved emission. We have elaborated MSA-CdSe QDs capped with mercaptosuccinic acid using various stoichiometric Cd/MSA ratios during the aqueous synthesis. Modulating the Cd/MSA ratio directly affects the size and photophysics of the QDs, in particular the fluorescence emission spectrum and decay. We rationalized the effect on QDs size by a change of the CdSe formation rate during synthesis. Acting on the Cd/MSA ratio appears a mean of modulating the emission spectrum and understanding the photophysical processes involved with respect to the QD structure.