<p>Seedbanks are a reservoir of plant diversity from which plants can regenerate. Seedbanks are particularly important in dynamic, disturbance-prone landscapes characterised by environmental variation. Understanding the composition of seedbanks and their role in standing vegetation dynamics provides insights into past and future vegetation change, including the potential for plant invasions under different scenarios. In disturbed ecosystems, seedbank composition is often overlooked as a critical component of invasion dynamics. Here, we investigate the composition of soil and litter seedbanks across riverine habitats (instream, riparian and floodplain) in the heavily modified agricultural landscapes of the northern Murray–Darling Basin, eastern Australia. Using germination trials, we examined spatial variation in native and non-native seedbank assemblages and explored likely environmental drivers of seedbank composition as well as similarity to the standing vegetation. Germinable seedbanks comprised 42 native and 34 non-native species. Native seedbanks were more abundant, species rich and functionally diverse, while non-native seedbanks were largely dominated by annual forbs and grasses. Non-native seedbank composition, particularly where the abundance and richness of germinable seeds was high, was associated with agricultural land use transformation and hydrological variation, reflecting the roles of disturbance, stochasticity and opportunism in invasion dynamics. Floodplain seedbanks harboured over 20% more non-native species than either riparian or instream habitats. Many native and non-native species were unique to either the seedbank (33 species) or standing vegetation (51 species), demonstrating the differences between these assemblages at the time of surveys. Current management does not adequately consider seedbank composition, overlooking its contribution to both native regeneration and invasion potential.</p>