This study compared the quality and antioxidant characteristics of water spinach (WS, Ipomoea aquatica Forsk.) cultivated in Korea using various cooking methods. First, the leaves and stems of WS were separated and cooked by blanching, boiling, steaming, or microwaving. The proximate composition, pH, total acidity, color, total polyphenol and flavonoid contents, and DPPH and ABTS radical scavenging activities were analyzed. The water content of WS was higher in the stems than in the leaves, while the crude protein, crude ash, crude fat, and carbohydrate contents were higher in the leaves. With all cooking methods, the pH increased, and the total acidity decreased; browning occurred during the cooking process. All antioxidant components and activities were higher in the WS leaves than in the stems. The total polyphenol and flavonoid contents were high in the leaves and stems of microwave-cooked WS; compared to the control, the antioxidant components were higher in the leaves than in the stems. The DPPH and ABTS radical scavenging activities were highest in the leaves and stems of microwave-cooked WS. The DPPH radical scavenging activity of the stems was high with boiling, while the ABTS radical scavenging activity was high with steaming. The cooking method selected is important because the nutrient content and antioxidant activities can differ according to the cooking method. This study provides basic information that could aid the use of WS as food.