Understanding how species respond to differences in resource availability is critical to managing biodiversity under the increasing pressures associated with climate change and growing human populations. Over the last century, the floodplain forests of Australia's largest river system, the Murray-Darling Basin, have been much affected by intensive harvesting of timber and firewood, and increasingly stressed by river regulation and, recently, an extended drought. Fallen timber – logs and shed branches – is known to play a key role in the ecology of several important species on these floodplains. Here, we monitored the response of the ant assemblages of a floodplain forest along the Murray River to a large-scale (34 ha) experimental manipulation of fallen-timber load (0 to 80 t ha−1) over 4 years. The forest was subjected to an incidental, extensive flood that enabled us to examine how two important stressors (timber removal and river regulation) affect ant assemblages. Ants showed little response to the proximity of fallen timber within plots, prior to the flood, or to different loads among plots, unlike other floodplain biota. After the flood, both ant abundance and species richness increased and species composition changed. However, this increase in species richness after flooding was less pronounced in plots with higher amounts of fallen timber. Managing river red gum forest using a mosaic of flood regimes, more representative of historical conditions, is likely to be the most effective way to maintain and enhance the diversity of ants and other biota on these important floodplains.