Continuous treatment of polyester/cotton blended fabric samples was carried with hexamethyldisiloxane (HMDSO) plasma on the pilot scale atmospheric pressure plasma reactor. The mixture of helium and argon was used as carrier gas for generating dielectric barrier discharge plasma. The effect of discharge power and treatment time on the water repellent properties of samples were evaluated with contact angle (CA) and spray test measurements. Spray test and CA results showed improved resistance to wetting with water. The effect of discharge conditions on the surface morphology and surface chemistry of plasma treated samples were investigated by scanning electron microscopy (SEM) and Fourier transform infrared (FTIR) spectroscopic analysis, respectively. The presence of Si-O-Si and Si-CH3 groups in the structure of plasma polymer deposited at the surface of P/C samples was revealed by FTIR spectroscopy. Further, structural differences in HMDSO plasma polymer deposited under different discharge conditions were reported with reference to organic/inorganic nature of plasma polymer. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2011.