Water-dispersible ZnSe nanocrystals (2–3 nm in diameter) producing photoluminescence (PL) in a blue region were prepared using several thiol-stabilizers. Thioglycerol (TG) gives the most intense PL having a shoulder at 387 nm and a maximum at 475 nm. The former was assigned to the excitonic emission, whereas the latter was assigned to a defect emission. Reflux increases the PL intensity, but did not change its peak wavelength significantly. TG plays an essential role in stabilizing the ZnSe colloidal solution, but it also creates defect emission. Therefore, the less the amount of surfactant, the more the PL intensity becomes in a range where the solution is not precipitated. The attachment and removal of TG on the surface of nanocrystals only occur at refluxing temperature (100 °C). On the other hand, removal of hydroxyl ions from the surface occurs at room temperature when pH is reduced. The ζ-potential and PL intensity are correlated strongly with the pH of the colloidal solution. This indicates hydroxyl ions passivate the surface significantly. Under optimized conditions of TG ratio and reflux time, the ZnSe nanocrystals in water produced whitish-blue emissions with an efficiency of 10% relative to rhodamine 6G. The nanocrystals in water are stable for months in a refrigerator.