The flooding regime of lowland river systems governs the distribution and abundance of floodplain vegetation by influencing the movement of propagules between the river channel and the floodplain, and through the creation of suitable habitat. The distribution of trees and shrubs in a floodplain depends on their tolerance to, and requirements for flooding. Floodplain vegetation is significantly affected by human activity, primarily through the changes to water regime resulting from damming, flow regulation, and flow extraction. Providing water as an environmental flow, to improve or maintain vegetation communities requires an understanding of the watering requirements of key floodplain species. This study describes an experiment to determine the relationship between inundation duration and the germination and recruitment of two shrub species common to the floodplains of the Murray Darling Basin: tangled lignum (Duma florulenta) and nitre goosefoot (Chenopodium nitrariaceum). Five inundation treatments were applied to the seeds of both species: rainfall, constantly soaked soil, 20, 40 and 60 days of inundation to a depth of 2.5 cm. Three additional treatments were applied to nitre goosefoot seeds: 5, 10 and 15 days of inundation. Tangled lignum established under all inundation scenarios with the highest germination occurring in the constantly soaked soil (43.5% ± 5.98) and lowest in the rainfall treatment (8.38% ± 2.02). Nitre goosefoot also established under all inundation scenarios, but the highest germination of seeds occurred after inundation of five days (17.25% ± 2.17) and the lowest occurred after inundation of 60 days (0.38% ± 0.24). These results support the observed distributions of these species across floodplains, tangled lignum occurs near semipermanent aquatic habitat and nitre goosefoot occurs on the flood margins. This information can be used by water resource managers looking to support floodplain vegetation communities with watering actions.