An aqueous route of synthesis is described for rapid synthesis of lead selenide quantum dots (PbSe QDs) at room temperature in an attempt to produce water-soluble and stable nanocrystals. Several thiol-ligands, including thioglycolic acid (TGA), thioglycerol (TGC), 3-mercaptopropionic acid (MPA), 2-mercaptoethylamine hydrochloride (MEA), 6-mercaptohexanoic acid (MHA), and l-cysteine (l-cys), were used for capping/stabilization of PbSe QDs. The effects of the ligands on the stability of PbSe QDs were evaluated for a period of two months at room temperature under normal light conditions and at 4 °C in the dark. The TGA- and MEA-capped QDs exhibited the highest stability prior to purification, almost two months when kept in the dark at 4 °C. However, the stability of TGA-capped QDs was reduced substantially after purification to about 5 days under the same conditions, while MEA-capped QDs did not show any significant instability. The stabilization energies of Pb-thiolate complexes determined by theoretical DFT simulations supported the experimental results. The PbSe QDs capped with TGA, MPA and MEA were successfully purified and re-dispersed in water, while those stabilized with TGC, MHA and l-cys aggregated during purification attempts. The purified PbSe QDs possess very susceptible surface resulting in poor stability for about 30-45 min after re-dispersion in water. In the presence of an excess of free ligand, the stability increased up to 5 days for TGA-capped QDs at pH 7.19, 9-12 days for MPA-capped QDs at pH 7.3-7.5 and 45-47 days for MEA-capped QDs at pH 7.35. X-Ray diffraction (XRD) results showed that the QDs possess a cubic rock salt structure with the most intense peaks located at 2θ = 25.3° (200) and 2θ = 29.2° (100). TEM images showed that the size of the QDs ranges between 5 and 10 nm. ICP-MS results revealed that Pb Se ratios were 1.26, 1.28, 3.85, 1.18, and 1.31 for the QDs capped with TGA, MPA, MEA, l-cys, and TGC, respectively. The proposed method is inexpensive, simple and utilizes environmentally friendly chemicals and solvents.