Dryland alluvial rivers are naturally complex systems with a range of in-stream and floodplain geomorphic units that provide habitat for aquatic and terrestrial biota. These systems are increasingly threatened by accelerated rates of sedimentation leading to declines in geomorphic complexity, habitat quality, and ponding depth. The implications of sedimentation on waterholes, or deep pools, is of particular concern, as they provide critical refugia in arid environments. However, sources of sediment entering and infilling waterholes, and the flow-on effects for habitat and water quality, are not well understood. This study addresses the potential for sediment derived from alluvial floodplain gullies to influence geomorphic change in dryland rivers. Alluvial floodplain gullies are often overlooked in comparison to more widely documented hillslope, or colluvial, gullies. Alluvial gullying is a prevalent feature of the Barwon-Darling River, one of Australia's longest and most important waterways in the northern Murray-Darling Basin (MDB). The estimated volume of sediment derived from floodplain gullies is 168 million m3, which far exceeds estimates used in past sediment budgets. Gully size and complexity varied from small, linear features to large, complex, branching gullies and the total number of gullies increased by ~40 % from the 1960s to 2000s. However, the more recent episodes of gullying (i.e., post 1960s) are limited to smaller gullies, which are likely to yield less sediment than the side walls of the older, larger, more complex gullies. Based on the average decline in maximum waterhole depth, ~19 million m3 of sediment has accumulated in Barwon-Darling waterholes over the past 120 years (equivalent to ~158,000 m3 a−1). A predictive relationship between gully volume and change in waterhole depth was expected, but not observed. Nevertheless, the role of alluvial floodplain gullies as a significant source of sediment should not be overlooked when assessing dryland river forms and processes. River management should consider the implications of changing sediment sources and in-stream loads, with associated changes in water quality and aquatic habitats, which influence river condition.