Microwave excited plasma source with slot antenna in water is a novel plasma applicable to materials processing in liquid. In order to apply this microwave plasma source to a practical use for solute decomposition, it is necessary to evaluate the decomposition efficiency for refractory organic solutes and understand the decomposition process of solution as well. In this paper, the microwave plasma treatment was demonstrated through decomposition of refractory organic solutes such as acetic acid, polyvinyl alcohol (PVA), and 4-chloro-2-methylphenoxy acetic acid (MCPA) in aqueous solutions. Total organic carbon concentration and high-performance liquid chromatography measurements revealed that the refractory organic substances such as acetic acid, PVA, and MCPA were decomposed by microwave plasma. Intermediate products of MCPA were investigated by gas chromatography coupled to a mass spectrometry and ion chromatograph during MCPA degradation using microwave excited plasma.