Wet season floods in the Daly River are an annual disturbance, of varying magnitudes, when river depths can exceed 10 m and current speeds exceed 1 m/s. During the wet season, shear stress and drag forces, as well as substrate loss, remove benthic algae and macrophytes from the riverbed. The standing stock of 6 groups of aquatic plants was determined over a 3.3 km reach, comprising 2 pools and 2 runs, during the dry season in July, September and November when river flow was groundwater-fed. These groups were benthic microalgae, benthic filamentous macroalgae (notably Spirogyra), Characeae, Vallisneria nana, Schoenoplexus and phytoplankton, though the latter two groups were always a minor proportion of the total standing stock. A preliminary survey in June revealed the presence of benthic algae, while macrophytes were not observed though remnants of Vallisneria and Schoenoplexus would have been present. The total standing stock, measured as chlorophyll a, increased over the dry season, approximately doubling every 2 months. Initially, benthic microalgae and filamentous macroalgae were the dominant plant. In the mid-dry season, the dominant plant shifted to Characeae, and then to Vallisneria at the end of the ‘dry’. This succession in aquatic plants and their contribution to the total standing crop is probably underpinned by the rates of algal colonisation, relative plant growth rates and carrying capacity, and the resilience of Vallisneria and Schoenoplexus to wet season flood disturbance.