Facilitated transport membranes (FTMs) comprising fixed carrier agents hold considerable potential for obtaining selective and fast separation of mixed molecules in either gas or liquid state. However, diffusion through the membrane is inevitably affected by the resistance from the polymer matrix, where the carrier is absent. Herein, a poly(vinyl alcohol) (PVA)-based separating layer combining the merits of fixed-site transport agents and inorganic nanofillers was developed to reduce the transport resistance. Carbon nanotubes (CNTs) with different degrees of oxidation were prepared and incorporated into the sulfonic acid (-SO3H)-modified PVA matrix. The resultant composite membrane consisting of a microporous polytetrafluoroethylene substrate and a thin PVA-based separating layer (∼700 nm thick) was subject to pervaporation desalination of sodium chloride solution (35,000 ppm) at 30 °C. The effect of -SO3H as a fixed transport agent in the PVA matrix was first investigated experimentally, showing an increase of water flux by 21.8% compared with a control membrane without the transport agent. Subsequently, the CNT-incorporated FTM exhibited good stability (50 h) and improvement in water transport, which was ∼161% of the control FTM (PVA with -SO3H) without loss of selectivity. Such high and stable performance achieved in the CNT-incorporated FTM originated from the construction of low-resistance transport pathways by CNTs between -SO3H groups as well as their uniform dispersion in the polymer matrix.