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This work was funded by CEF (Centro de Estudo Florestais, Instituto Superior de Agronomia, Universidade de Lisboa (UIDB/00239/2020) and the project PORBIOTA (e-infrastructure for information and research on Biodiversity (POCI-01-0145-FEDER-022127), supported by Operational Thematic Program for Competitiveness and Internationalization (POCI), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (FEDER). Authors are also grateful to the Herdade da Machoqueira do Grou for permission to undertake research.

The Data set contains eddy covariance measurements of carbon and water fluxes and ancillary measurements observed at a cork oak woodland (Quercus suber L.) in central Portugal. The climate is Mediterranean, with mild, wet winters and hot, dry summers. Data are available in the file data.csv (UTF-8 encoding), the description of the variables and units are available in the file meta.csv (UTF-8 encoding). Further description of the site, methods and data processing can be viewed in the files metadata.pdf and metadata.csv