Small mammal responses to flooding in the lower Missouri River floodplain are poorly understood. Our study examined the survival of marked populations of small mammals in mature and regenerating forest seral stages in response to a brief flood. Peromyscus spp. were the most abundant species captured before (94% of individuals captured) and after (98%) the flood and survival in inundated mature forest sites did not significantly differ from unflooded reference sites. However, the lowest number (n = 14) and percentage (29%) of Peromyscus spp. recaptures occurred in a young regenerating forest site. Elliot's short-tailed shrews (Blarina hylophaga), which are less adapted for arboreal habitats, declined in abundance after the flood.