CdTe/CdS core/shell quantum dots (QDs) are formed in aqueous synthesis via the partial decomposition of hydrophilic thiols, used as surface ligands. In this work, we investigate the influence of the chemical nature (functional group and chain length) of the used surface ligands on the shell formation. Four different surface ligands are compared: 3-mercaptopropionic acid, MPA, thioglycolic acid, TGA, sodium 3-mercaptopropanesulfonate, MPS, and sodium 2-mercaptoethanesulfonate, MES. The QD growth rate increases when the ligand aliphatic chain length decreases due to steric reasons. At the same time, the QDs stabilized with carboxylate ligands grow faster and achieve higher photoluminescence quantum yields compared to those containing sulfonate ligands. The average PL lifetime of TGA and MPA capped QDs is similar (≈20 ns) while in the case of MPS shorter (≈15 ns) and for MES significantly longer (≈30 ns) values are measured. A detailed structural analysis combining powder X-ray diffraction, and X-ray photoelectron spectroscopy (XPS) indicates the existence of two novel regimes of band alignment: in the case of the mercaptocarboxylate ligands the classic type I band alignment between the core and shell materials is predominant, while the mercaptosulfonate ligands induce a quasi-type II alignment (MES) or an inverted type I alignment (MPS). Finally, the effect of the pH value on the optical properties was evaluated: using a ligand excess in solution allows achieving better stability of the QDs while maintaining high photoluminescence intensity at low pH.