Cold atmospheric pressure plasma (CAP) oxidizes organic compounds in water through thegeneration of a variety of reactive species including O-3 and OH radicals. While the energy efficiency and rate of decomposition of the chemical compound in water is already extensively studied, only few studies focused on the reactive species responsible for the decomposition. We reporton an investigation of the chemical reactive species involved in the decomposition of crystal violet (CV), a model organic compound, by an RF driven plasma jet in different gas mixtures. Different gas mixtures lead to different concentrations of reactive species responsible for the decolorization of CV. Moreover, the effect of transport limitations on the efficiency of the plasma treatment is reported. A study of positive control measurements, the effect of scavengers of relevant reactive species and particle imaging velocimetry reveal the dominant role of short-lived species at the plasma-liquid interface in which OH most likely plays an important role. Moreover, the decolorization rate is limited by transport of CV to the near boundary region. The results suggest that for the optimization of water treatment by the short-lived species generated by a plasma, an optimum transport of the to-be-treated compounds to the interface might be more critical than effective reactive species production in the plasma.