This dataset presents greenhouse gas emissions data from controlled peat mesocosm experiments conducted between February 2023 and December 2025. The study investigated carbon dioxide (CO₂) and methane (CH₄) emissions from drained peat soils collected from three sites in the East Anglian Fens, UK, by researchers at the Department of Earth Sciences, University of Cambridge. The experiments were carried out in laboratory mesocosms to examine how changes in water table levels influence greenhouse gas fluxes and porewater chemistry. CO2 and CH4 emission data are provided for "short-term" experiments in which columns of drained peat were subjected to a high water table and then gradually drained over ~50 days with CO2 and CH4 emissions monitored as the water table is lowered. CO2 and CH4 emission and pore fluid concentration data are provided for "long-term" experiments in which mesocosms of drained peat were subjected to high water table (5cm above the soil surface) for a period of around 5 months. These data were generated to improve understanding of how peatland rewetting and water table management affect greenhouse gas dynamics in lowland fen systems, supporting assessments of peatland restoration and climate mitigation strategies. This work was carried out as part of the Centre for Landscape Regeneration at the University of Cambridge (Landscape Regeneration Solutions to the Interlinked Extinction and Climate Crises that support Sustainable Development, NE/W00495X/1) with analytical facilities funded by LASER-ENVI - A LASER spectrometer based ENVIronmental Gas and Gas-Isotope Facility (NE/V015435/1). Full details about this dataset can be found at https://doi.org/10.5285/0cefa296-33ad-4a73-8783-3471c6f64ee7