Abstract: Plants grown in coastal and estuarine riparian zones are vulnerable to combined waterlogging and salt stresses. In this study, three stress treatments, including waterlogging, salinity (350 mmol/L), and combined salinity-waterlogging (175 mmol/L), were used to compare the eco-physiological responses of Cleistocalyx operculatus (Roxb.) Merr. et Perry and Syzygium cumini (L.) Skeels seedlings, two plant species with strong waterlogging tolerance, to different stress conditions. Results showed that after 24 d, plant height growth, leaf area, total biomass, root activity, net photosynthetic rate (P_n), transpiration rate (T_r), and stomatal conductance (G_s) decreased in both species under all three treatments, while leaf relative conductivity and peroxidase (POD) activity increased. In the waterlogging treatment, intercellular CO₂ concentration (C_i) continuously declined with treatment duration in both species. In the salinity treatment and combined salinity-waterlogging treatment, C_i decreased at first and then increased. Compared to the waterlogging treatment, the combined salinity-waterlogging treatment resulted in a significant reduction in leaf area, total biomass, P_n, T_r, and G_s in both species, but a significant increase in root shoot ratio, relative conductivity, and POD activity. Compared with S. cumini, C. operculatus seedlings formed adventitious roots after 24 d of waterlogging treatment, and exhibited higher root, and POD activities, with less membrane damage. Thus, C. operculatus possessed stronger waterlogging resistance than S. cumini. However, compared to C. operculatus seedlings, S. cumini demonstrated higher leaf area, biomass, root activity, photosynthesis efficiency, superoxide dismutase and POD activities, but lower malondialdehyde content under salinity and combined salinity-waterlogging treatments. Therefore, S. cumini showed stronger salt tolerance compared to C. operculatus.