This study investigated five typical wetland plants in Dongting Lake—Acorus calamus, Zizania latifolia, Phragmites australis, Carex brevicuspis, and Typha orientalis—under different flooding durations (30, 60, 90, and 120 days), systematically analyzing their morphological and physiological responses as well as nitrogen and phosphorus removal efficiency. The results showed that flooding duration significantly influenced plant morphology, physiological responses, and nutrient removal efficiency. Morphologically, with increasing flooding time, the biomass and plant height of A. calamus decreased significantly; the biomass and root length of C. brevicuspis remained relatively stable while plant height slightly decreased; whereas the plant heights of P. australis, Z. latifolia, and T. orientalis continued to increase with prolonged flooding. Physiologically, markers of oxidative stress and osmoregulation showed species-specific trends. For instance, in Z. latifolia, contents of malondialdehyde (MDA) and soluble sugars decreased significantly, while antioxidant enzyme activity and chlorophyll content increased. In contrast, T. orientalis displayed a dynamic change in MDA, superoxide dismutase (SOD), and proline, which decreased initially, peaked at 90 days, and then declined again, whereas its chlorophyll content continuously decreased. Regarding purification capacity, the nitrogen and phosphorus removal rates of P. australis and T. orientalis continuously improved with prolonged flooding. In contrast, A. calamus, Z. latifolia, and C. brevicuspis reached peak removal efficiency at 60–90 days of treatment before declining. In summary, different plants exhibited significant species-specific and time-dependent responses in morphology, physiology, and function under flooding conditions. P. australis and T. orientalis can maintain high purification efficiency under prolonged flooding, making them more suitable as dominant species for long-term flooded wetland ecosystems.