Effects of large-scale flooding on forest composition and structure are a function of flood duration, depth, timing, and frequency. Throughout the Upper Mississippi River System (UMRS), floods in 1993 and 2019 were record-setting events followed by high rates of tree mortality. These events generated interest in species adaptations to flood event characteristics and how forest communities have changed in response to large-scale floods. We investigated associated tree mortality, how the floods differed spatially, and how floodplain forest communities have changed since 1993. Eight UMRS reaches were surveyed in a 1995 study, documenting vegetation species composition, size, and abundance. In 2021, a selection of plots (63%) were revisited and surveyed to quantify 2019 flood effects. For each site, we extracted daily inundation data for flood years and preceding decades from a surface water inundation model. We found post-flood mortality varied spatially and generally reflected inundation duration patterns. Lower latitude reaches experienced longer inundation durations and greater tree mortality in 1993 than in 2019, while higher latitude reaches experienced similar inundation duration and depth and similar mortality between events. Decadal inundation attributes also differed. During 2009–2018, inundation duration was greater and events occurred later than during 1983–1992 in all reaches. Most forest trajectories were Acer saccharinum-dominated and changed relatively little in species composition and structure. The greatest change in composition occurred at plots with high mortality from the 1993 flood, particularly in more flood-prone locations or where there were many small-diameter individuals. In plots dominated by either Quercus spp. or Populus deltoides, species importance shifted toward more shade and flood-tolerant species after 1995 surveys. Self-replacement of these species may be limited by a change in regeneration conditions resulting from an ongoing inundation regime shift in the case of Quercus spp., or succession to more shade-tolerant species in the case of Populus communities. Overall, effects on floodplain forests from the two flood events were heterogeneous. In some cases, forest change was likely just as influenced by shifts in flood regime as it was from singular flood events.