The Apalachicola-Chattahoochee-Flint (ACF) River basin is an important ecological and economic component of a three-state region (Florida, Alabama and Georgia) in the southeastern U.S. Along the Apalachicola River in northwest Florida, the duration of floodplain inundation has decreased as a result of declining river levels. Spring and summer flows have diminished in volume because of water use, storage and evaporation in reservoirs, and other anthropogenic and climatic changes in the basin upstream. Channel erosion from dam construction and navigation improvements also caused river levels to decline in an earlier period. In this paper, we document trends in floodplain forest tree species composition for the interval spanning these influences. Historic tree inventories from the 1970s were compared to present-day forests through non-metric multidimensional scaling, indicator species analysis (ISA) and outlier detection. Forests are compositionally drier today than in the 1970s. Overstory to understory compositional differences within habitats (levees, high/low bottomland forest and backswamps) are as large as the species contrasts between habitats. Present-day forests are also compositionally noisier with fewer indicator species. The largest individual declines in species density and dominance were in backswamps, particularly for Fraxinus caroliniana Nyssa ogeche and Nyssa aquatica. We discuss how contrasts in the compositional change signal for levee and backswamp landform habitats reflect a complex biogeomorphic response to fluctuating river flows for alluvial rivers in humid climates.