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Lake Neusiedl, a shallow brackish lake of Austria and Hungary, is the westernmost steppe lake of Europe with an area of ca. 320 km² and the second largest coherent reed population in Europe. Half of Lake Neusiedl consists of a wetland ecosystem dominated by Phragmites australis, which forms a seasonally varying mosaic of water, reed and sediment patches, is highly sensitive to climate variations and which we investigated here.Little is known about the effects of climate change on reed dominated wetlands and the contribution of central European reed belts as a source of greenhouse gases (GHG). The current ongoing drought periods at Lake Neusiedl affect especially the water balance but also the carbon fluxes in the reed belt. Therefore, we investigated the drought influenced carbon and water fluxes and their drivers of the reed ecosystem of a brackish lake over the last three years.We used the eddy covariance (EC) technique to continuously quantify the vertical turbulent GHG exchange between the reed belt and atmosphere. The EC observations have been conducted near Illmitz in the natural zone of National Park Lake Neusiedl from summer 2018 to now. For taking the reed development of the studied ecosystem into account, vegetation indices data were used.The annual CO2 emissions decreased by 95 % from 200.5 g C m-2 in 2019 to 9.2 g C m-2 in 2021. Gross primary production and ecosystem respiration both increased from 2019 to 2021. The annual emissions of CH4 decreased by 59 % from 9.0±1.0 g C m-2 in 2019 to 3.7±1.9 g C m-2 in 2021. The reed belt tended from a strong to a low carbon source if only the vertical flows are taken into account. One explanation is the decreasing water level in the lake between 2019 to 2021, which was followed by a drying out of the reed belt (≙ no water above surface) in the late summer of 2020 and a longer period in 2021. The second explanation is the increasing reed growth (in area and biomass) inside the reed belt which increased the photosynthetic rate. The vegetation indices like NDVI, EVI and LAI from the reed belt support this by an increasing tendency from 2019 to 2021. The third explanation is that due to the low water levels less (or almost no) lateral exchange occurred via channels between the reed belt and the open water areas of the lake in 2021 compared to 2019.The apparent disconnection between the open water area of Lake Neusiedl and the reed belt re-directs carbon cycles and ecosystem functioning.