In recent years an increasing number of streams have been restored to improve conditions for natural fen and meadow vegetation to develop in the associated riparian areas, but with modest success. Here we apply a controlled and replicated approach to investigate the role of flooding, sediment deposition, and seed addition for species recruitment in riparian areas with different types of standing vegetation. We expect that species recruitment is restricted in areas where the vegetation is dominated by fast-growing productive species because competition for light will make the establishment of new species difficult, especially for low-productive target species. We found that the naturally recruited species were few, mostly common, and widely distributed species. A majority of the recruited species, including target species added as seeds into the sediments, emerged in all areas independent of the characteristics of the standing vegetation. We observed significant temporal changes in compositional patterns throughout the experimental period (May to October). These changes were especially pronounced in areas with fen/fen-meadow vegetation and were closely associated with the emergence and growth of species originating from the deposited sediments (e.g. Equisetum pratense, Poa trivialis, Urtica dioica), including the seeded target species (Lychnis flos-cuculi and Lotus pedunculatus) and with a decline in fen-associated mosses and small sedges. Compositional changes were also associated with shifts toward more productive species in areas previously dominated by low and intermediately productive species. We infer that flooding and sediment deposition play a limited role for recruitment of target species in riparian areas and that sediment deposition may entail a risk of losing diversity in riparian areas.