Due to anthropogenic climate change, climate observations over the last decades show an increase of global land and sea surface temperature.This is accompanied by unpredictable consequences like extreme weather events, sea level rise, droughts or flooding, which canlead to risks for animals and humans in the according region. To reduce the risks of flooding for settlements an area at the Morava Riverwas restored into a floodplain area including near natural riparian forests, water bodies and diverse meadows. The restoration changed theability of the wetland to act as a carbon sink or source. Thus, a quantification of the real performance of such a specific ecosystem will beconducted. Besides the monitoring of flora and fauna (including the natural grazing by wild horses and temporarily cattle) done by WWF anew measurement setup to quantify CO2, H2O, CH4 fluxes on an ecosystem level based on the Eddy Covariance (EC) method was installedon a floating platform by researchers from the BOKU in the framework of the Horizon Europe project REWET. This paper gives advices andpoints out the challenges of setting up an EC system in regularly flooded areas and in a clear-cut of a forest. Besides the ecological restorationand the reduction of risk of flooding, these measurements aim to investigate the potential of the restored floodplain area to mitigateclimate change in terms of acting as a source or sink for carbon.