Regulation of river flows has altered floodplain ecosystems around the world. Floods are less frequent, which leads to reduction of favourable environmental conditions for many terrestrial and aquatic organisms adapted to natural flooding regimes. In Australia, the Murray River floodplains have been subjected to decline in inundations, to extensive logging and to removal of fallen timber. The yellow-footed antechinus (Antechinus flavipes) is the only small, native, ground-dwelling/semi-arboreal mammal on most floodplains of south-eastern Australia, yet the effects of floods on its population dynamics largely are unknown. Here, we found positive effects of proximity to flooding, higher woodloads and of abundance of large, hollow-bearing trees on antechinus numbers. Mean trapping rates of antechinuses were lowest in 2003 following a 3-year period with no inundation, higher in 2004 following the first breeding season during a small, controlled flood in 2003, and higher again in 2005, following a small, controlled flood in 2004. In 2004 and 2005, trapping rates declined with distance from floodwaters. This study provides evidence for the benefits of using management flows to inundate floodplains, conserving large trees and ensuring high woodloads in floodplains for sustaining populations of the yellow-footed antechinus.