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Health issues in elderly individuals are often complex and tend to lead to chronic diseases; such issues can be due to a decline in fitness resulting from lack of physical activity. Aqua exercise and burdock are positive effects on cardiovascular disease and vascular health. This study investigated the changes due to aqua exercise and burdock extract intake in senior fitness, prostaglandin I2 (PGI2), and thromboxane A2 (TXA2) in elderly women. Forty elderly women (65–80 years) volunteered for this study. After baseline measurements, participants were randomized into control (n = 8), aqua exercise (n = 11), aqua exercise and burdock extract intake combination (n = 11), and burdock extract intake groups (n = 10). The variables of senior fitness tests, PGI2 and TXA2 were measured in all participants before and after the 12-week study. Blood collections were carried out at the beginning- and the end of aqua exercise training. Muscular strength, endurance, flexibility, and cardiorespiratory endurance of aqua exercise and burdock extract intake group at post-test significantly increased compared to pre-test (p<0.05). There were no significant differences in PGI2 and TXA2 between pre- and post-training programs. In conclusion, our findings indicated that the aqua exercise and burdock extract intake improves senior fitness factors in elderly Korean women. Also, the program participation led to a balance between PGI2 and TXA2. Additionally, burdock extract intake may be useful in vascular health by playing a secondary role in disease prevention and health promotion.