Juvenile plants often have tight microhabitat associations because of specific requirements for seed germination and subsequent establishment. Due to their larger size, adults may be more adept at coping with stress. However, few studies consider the role of ontogeny in structuring plant populations, even though phenotypic expression can change through life history. In cypress-tupelo swamps of the United States, understory species often grow on microsites above floodwaters. In a field survey of one such species, Itea virginica, we found that more than 98% of seedlings occurred on elevated microsites, which were relatively infrequent. However, this strict association relaxed through ontogeny, with nearly 8% of subadults and adults rooted directly on the forest floor. We hypothesized that flooding inhibits juvenile establishment on the forest floor. In greenhouse experiments, we investigated the effects of flooding and substrate on Itea performance. Seeds had similar germination rates on drained swamp soil and cypress knee wood. Seedling growth was high on unflooded soil, but declined precipitously when submerged. Finally, performance of seedlings, but not older plants, decreased with flood severity. Our results highlight the importance of assessing stress tolerance over multiple life history stages because limitations of juveniles can constrain the distribution patterns of future ontogenetic stages.