Electrical pulsed discharge plasma produces various powerful oxidizing agents, such as hydroxyl radicals and ozone, which have high oxidation potential. These species play an important role in the decomposition of persistent organic compounds in wastewater. Because highly concentrated oxidants are directly produced inside the plasma, plasma realizes high-speed wastewater treatment without pretreatment of samples, such as pH adjustment. The pulsed discharge plasma generated over the water surface and inside bubbles is highlighted as a highly efficient method for plasma generation and radical supply into wastewater. In this paper, the physical and chemical properties of the discharge plasma generated over a water surface are described. The decomposition of persistent organic compounds dissolved in wastewater, such as 1,4-dioxane, formic acid, and dichloromethane, by plasma discharge is demonstrated, and their mechanisms are discussed. These persistent compounds, which have strong toxicity and stability, can be efficiently decomposed and removed quickly from solutions by plasma treatment. Furthermore, the treatment of nutrient solutions used in hydroponic systems for plant cultivation is also introduced as a novel application of plasma, and the effects of bacterial inactivation, decomposition of allelochemicals, and improvement in plant growth by plasma are demonstrated.