We demonstrate the origin and mechanism of the hysteresis behavior that is frequently observed during the operation of organic field-effect transistors (OFETs) based on polymer gate dielectrics. Although polar functionalities, such as hydroxyl groups, present in the polymer gate dielectrics are known to induce hysteresis, there have only been a few detailed investigations examining how the presence of such end functionalities both at the polymer surface—forming an interface with the semiconductor layer—and in the bulk influences the hysteresis. In this study, we control the hydrophobicity of the polymer by varying the number of hydroxyl groups, and use an ultrathin polymer/SiO2 bilayer and a thick single polymer as the gate dielectric structure so that the hysteresis behavior is divided into contributions from hydroxyl groups present at the polymer surface and in the bulk, respectively. Electrical characterizations of the OFETs, performed both in vacuum (≈10−3 Torr) and in ambient air (relative humidity of about 40%), show that the observed hysteresis is determined by the transport of water within the polymer (i.e., the adsorption at the polymer surface and the diffusion into the bulk), which in turn is controlled by the hydrophobicity and the thickness of the polymer.