In this paper, we propose a method for removing phenols and p-nitrophenols (PNPs) from flowing aqueous solutions generated by atmospheric pressure plasma jets (APPJs). For analyzing the removal characteristics, multiple techniques were used, including flow speed analysis of the aerated solution, optical emission spectroscopy (OES), and liquid chromatography. In addition, the reaction kinetics of diffusion and activation control processes were evaluated using aerated fluid speed variation and the corresponding activation energy. From these results, the relative intensities of hydroxyl radicals produced by an APPJ in water were found to be stronger than those in air and to decrease with increasing flow speed. Furthermore, the reaction kinetics were found to be diffusion-controlled when the solution flow speed was low and activation-controlled under high solution flow speed. It was also found that the degradation efficiency was enhanced with increasing flow speed, which increased the discharge voltage and temperature of the solution and changed the initial pH value when TiO2/UV catalysis was used. From the complex relationship between the reactive species, fluid diffusion, and discharge parameters in wastewater described herein, it is anticipated that these findings will facilitate new approaches to both the design and optimization of discharge reactors intended for wastewater treatment.