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Riparian zones are complex disturbance-mediated systems that are highly susceptible to invasion by alien plants. They are prioritized in most alien-plant management initiatives in South Africa. The current practice for the restoration of cleared riparian areas relies largely on the unaided recovery of native species from residual individuals and regeneration from soil-stored seed banks. Little is known about the factors that determine the effectiveness of this approach. We need to know how seed banks of native species in riparian ecosystems are affected by invasion, and the potential for cleared riparian areas to recover unaided after clearing operations. Study sites were selected on four river systems in the Western Cape: the Berg, Eerste, Molenaars and Wit Rivers. Plots were selected in both invaded ( >75% Invasive Alien Plant (IAP) canopy cover) and un-invaded (also termed reference, with < 25% IAP canopy cover) sections of the rivers. Replicate plots were established at two elevations (mountain stream and foothill) and in three moisture regimes (dry, wet and transitional bank zones). Soil samples were taken, surveys were done of the aboveground vegetation, and comparisons were made between invaded and non-invaded sites. Seed bank communities were clearly defined by the state of the river (reference or invaded) and moisture regimes (wet and dry bank zones). Comparisons at a landscape scale showed no clear pattern, as the composition of both aboveground and seed bank species assemblages were strongly influenced by site history, especially the extent of invasion and fire frequency. Even after heavy and extensive invasion, riparian seed banks have the potential to initiate the restoration process. However, not all riparian species are represented in the seed bank. Based on these results, restoration recommendations are outlined for alien-invaded riparian zones.