Core and core-shell quantum dots are covered with a layer of organic ligands which prevents aggregation and eliminates surface defects, thus enhancing the photophysical properties and stability of the material. These ligands are usually Lewis bases and can therefore be affected by the presence of acid in the surrounding environment. We synthesized core CdSe and core-shell CdSe-ZnS quantum dots with various shell thicknesses and different organic ligands, and we investigated the effect of acid and base on their photophysical properties. In dilute CHCl3 solution, the organic ligands can be protonated upon addition of acid and detached from the surface of the nanoparticles. As a consequence, the nanoparticles aggregate and their luminescence is quenched. Aggregated particles can be partly disgregated and the luminescence restored by deprotonation of the free ligands with a base. Since the presence of organic ligands on the surface is an essential characteristic of quantum dots, these effects should be taken into consideration when designing quantum dot-based sensors.