Abstract. Rewetting drained peatlands for paludiculture purposes is a way to reduce peat oxidation (and thus CO2 emissions) while at the same time it could generate an income for landowners, who need to convert their traditional farming into wetland farming. The side effect of rewetting drained peatlands is that it potentially induces high methane (CH4) emissions. Topsoil removal could reduce this emission due to the removal of easily degradable carbon and nutrients. Another way to limit CH4 emissions is the choice in paludiculture species. In this study we conducted a field experiment in the coastal area of the Netherlands, in which a former non-intensively used drained peat grassland is rewetted to complete inundation (water table ∼ +18 cm) after a topsoil removal of ∼ 20 cm. Two emergent macrophytes with high potential of internal gas transport (Typha latifolia and Typha angustifolia), and a free floating macrophyte (Azolla filiculoides), were introduced and intensive measurement campaigns were conducted to capture CO2 and CH4 fluxes as well as soil and surface water chemistry. Greenhouse gas fluxes were compared with a high-productive peat meadow as a reference site. Topsoil removal reduced the amount of phosphorus and iron in the soil to a large extent. The total amount of soil carbon per volume stayed more or less the same. The salinity of the soil was in general high, defining the system as brackish. Despite the topsoil removal and salinity, we found very high CH4 emissions for T. latifolia (84.8 g CH4 m−2 yr−1) compared with the much lower emissions from T. angustifolia (36.9 g CH4 m−2 yr−1) and Azolla (22.3 g CH4 m−2 yr−1). The high emissions can be partly explained by the large input of dissolved organic carbon into the system, but it could also be caused by plant stress factors like salinity level and herbivory. For the total CO2 flux (including C-export), the rewetting was effective, with a minor uptake of CO2 for Azolla (−0.13 kg CO2 m−2 yr−1) and a larger uptake for the Typha species (−1.14 and −1.26 kg CO2 m−2 yr−1 for T. angustifolia and T. latifolia, respectively) compared with the emission of 2.06 kg CO2 m−2 yr−1 for the reference site. T. angustifolia and Azolla, followed by T. latifolia, seem to have the highest potential for reducing greenhouse gas emissions after rewetting to flooded conditions (−1.4, 2.9, and 10.5 t CO2 eq. ha−1 yr−1, respectively) compared with reference drained peatlands (20.6 t CO2 eq. ha−1 yr−1). When considering the total greenhouse gas balance, other factors, such as biomass use and storage of topsoil after removal, should be considered. Especially the latter factor could cause substantial carbon losses if not kept in anoxic conditions. When calculating the radiative forcing over time for the different paludicrops, which includes the GHG fluxes and the carbon release from the removed topsoil, T. latifolia will start to be beneficial in reducing global warming after 93 years compared with the reference site. For both Azolla and T. angustifolia this will be after 43 years.