Knowledge of how germination and seedling establishment respond to soil water condition is crucial for plant conservation under global warming and land-use changes. We tested the flooding and drought tolerance of two plant species with different occurrences along a soil water gradient by assessing seed germination, seedling survival, seedling growth, and root characteristics. In the high Sino-Himalayas, Rheum alexandrae typically occurs in wetlands, R. nobile in scree or open slope with well-drained soils. Seeds and seedlings of the two species were subjected to different soil water conditions in controlled greenhouse experiments. Seed germination in both species was inhibited by high soil water content; however, seeds of R. alexandrae were more tolerant to flooding, especially to submergence. Seedling survival, biomass accumulation, root diameter, and root porosity of R. alexandrae increased significantly with increased soil water content, but submergence was lethal for seedlings. Seedling survival, biomass accumulation, and root length of R. nobile increased significantly in response to reduced soil water content. These results indicate that in the two species, seed germination and seedling establishment in response to different soil water condition are habitat-specific. Because both species are susceptible to moderate changes in soil water condition, their species-specific requirements with respect to this factor should be a consideration when planning their conservation.