Successful transfer of near-infrared emitting quantum dots (QDs) into water is critical for many biological applications. In this paper, PbS QDs capped by several types of most commonly used capping ligands are, transferred from an organic solvent into water via poly(maleic anhydride-alt-1-octadecene)-co-poly(ethylene glycol). It is found that the variation of the structure and optical property of QDs upon water transfer highly depends on the type of capping ligands because of their different interactions with their surroundings (such as solvent molecules, polymers, and QD surface). This is in clear contrast to the common concept that amphiphilic polymers will not disturb the ligand structure on the QD surface during the transfer process, and thus the type of ligands will not bear any direct relevance with the variation of QDs and their properties. This work demonstrates that when oleic acid (OA) or OA/trioctylphosphine (TOP) ligands are used, the amphiphilic polymer approach is able to maintain the initial QD structure and high photostability in water; whereas, in the case of oleylamine (OLA) ligands, severe ligand etching takes place, which initiates Ostwald ripening, leading to double size distribution and, moreover, the total photoluminescence (PL) loss in a short time after water transfer. The complete darkening of PbS capped by OLA QDs is found to be mainly due to the introduction of many unpassivated surface atoms during the etching and Ostwald ripening process. Among all the samples, PbS QDs capped by OA/TOP ligands show the highest PL intensity, doubling that of PbS QDs capped by OLA or OA ligands after immediate water transfer. Meanwhile, the PL spectral shift after water transfer also varies among the samples. Our study suggests that the surface ligands do play a crucial role in the process of water transfer of PbS QDs, and "correct" ligands should be used to obtain high-quality water-soluble PbS QDs using the amphiphilic polymer approach.