The eddy covariance data describes the fluxes of CO2, latent energy, and sensible heat. It also includes ancillary data: air and soil temperatures, net radiation balance, down-welling photosynthetically active radiation, wind speed, wind direction, vapour pressure deficit, friction velocity, Monin-Obukhov stability and modelled respiration. Data collection was carried out at Abbotts Hall marsh from the 15 December 2012 till the 27 January 2015. The Abbotts Hall site is in Essex, South East England, and the meteorological tower was situated in the middle of the marsh. This data was collected as part of Coastal Biodiversity and Ecosystem Service Sustainability (CBESS): NE/J015644/1. The project was funded with support from the Biodiversity and Ecosystem Service Sustainability (BESS) programme. BESS is a six-year programme (2011-2017) funded by the UK Natural Environment Research Council (NERC) and the Biotechnology and Biological Sciences Research Council (BBSRC) as part of the UK's Living with Environmental Change (LWEC) programme.