The recruitment of wood from the riparian zone to rivers and streams provides a complex habitat for aquatic organisms and can influence both aquatic biodiversity and ecosystem function. The Daly River in the wet–dry tropics of northern Australia is a highly seasonal, perennially flowing sand-bed river where surveys of river wood aggregations at the reach scale (~2 km) in 2008 and 2009 recorded densities of 37–78 km−1 and identified distinct types of river wood aggregations: key pieces, standing trees, fallen trees, wrack and single pieces. After larger than average flows in the 2008/2009 wet season, between 46% and 51% of the surveyed river wood had moved. The distribution of wood age classes indicated continual recruitment and slow turnover of wood within the river. Surveys of fish and habitat characteristics at the mesohabitat scale (~100 m) showed fish species richness; diversity and fish abundance were not correlated to the proportion of wood present. Fish assemblage structure was associated with wood cover as well as other environmental variables such as stream width and depth. The importance of in-stream wood also varied for different species and age classes of fish. This study documents the dynamic nature of river wood aggregations and their complex and variable distribution and suggests their importance as fish habitat in this tropical river. Copyright © 2012 John Wiley & Sons, Ltd.