How will coastal soils in areas newly flooded with seawater function as habitat for benthic marine organisms? This research question is highly relevant as global sea level rise and coastal realignment will cause flooding of soils and form new marine habitats. In this study, we tested experimentally the capacity of common marine polychaetes, Marenzelleria viridis, Nereis (Hediste) diversicolor and Scoloplos armiger to colonize and modify the biogeochemistry of the newly established Gyldensteen Coastal Lagoon, Denmark. All tested polychaetes survived relatively well (28–89%) and stimulated carbon dioxide release (TCO2) by 97–105% when transferred to newly flooded soils, suggesting that soil characteristics are modified rapidly by colonizing fauna. A field survey showed that the pioneering benthic community inside the lagoon was structurally different from the marine area outside the lagoon, and M. viridis and S. armiger were not among the early colonizers. These were instead N. diversicolor and Polydora cornuta with an abundance of 1603 and 540 ind m-2, respectively. Considering the species-specific effects of N. diversicolor on TCO2 release and its average abundance in the lagoon, we estimate that organic carbon degradation was increased by 219% in the first year of flooding. We therefore conclude that early colonizing polychaetes modify the soils and may play an important role in the ecological and successional developments, e.g. C cycling and biodiversity, in newly flooded coastal ecosystems. Newly flooded soils have thus a strong potential to develop into well-functioning marine ecosystems.