The impact of pulse-modulated generation of atmospheric pressure plasma on the efficiency of organic dye degradation has been investigated. Aqueous samples of methyl orange were exposed to low temperature air plasma and the degradation efficiency was determined by absorbance spectroscopy. The plasma was driven at a constant frequency of 35 kHz with a duty cycle of 25%, 50%, 75% and 100%. Relative concentrations of dissolved nitrogen oxides, pH, conductivity and the time evolution of gas phase ozone were measured to identify key parameters responsible for the changes observed in degradation efficiency. The results indicate that pulse modulation significantly improved dye degradation efficiency, with a plasma pulsed at 25% duty showing a two-fold enhancement. Additionally, pulse modulation led to a reduction in the amount of nitrate contamination added to the solution by the plasma. The results clearly demonstrate that optimization of the electrical excitation of the plasma can enhance both degradation efficiency and the final water quality. (C) 2014 Elsevier B.V. All rights reserved.