The regeneration process is a sensitive period within life cycles of floodplain tree species and can strongly influence forest community composition. Yet, fundamental information remains limited on the relationship between regeneration processes and the flood disturbances that, together, construct floodplain forest landscapes. In a controlled greenhouse experiment we tested the effects of complete submergence on six temperate floodplain forest species to understand how flood timing and duration influence seedling survival. Groups of overcup oak (Quercus lyrata), Nuttall oak (Quercus texana), willow oak (Quercus phellos), sugarberry (Celtis laevigata), green ash (Fraxinus pennsylvanica), and American elm (Ulmus americana) seedlings were submerged for either 5, 15, 25, or 0 days (control) at the ages of 3-weeks, 6-weeks, and 9-weeks post-emergence. All species demonstrated a higher sensitivity to flooding at age 3-weeks compared to 6- and 9- weeks, indicating substantial changes in seedling resilience within the first months following emergence. Additionally, the heavier-seeded Q. lyrata, Q. texana, and Q. phellos were less or equally vulnerable to flooding compared to the lighter-seeded C. laevigata, F. pennsylvanica, and U. americana across all age groups, especially at 3-weeks post-emergence. The results of this study have implications for understanding woody species regeneration ecology and changes in floodplain forest composition, particularly in the context of hydrologic modifications.