This data release consists of flux tower measurements of the exchange of energy and mass between the surface and the atmospheric boundary-layer in semi-arid eucalypt woodland using eddy covariance techniques. It been processed using PyFluxPro (v3.3.3) as described in Isaac et al. (2017), https://doi.org/10.5194/bg-14-2903-2017. PyFluxPro takes data recorded at the flux tower and process this data to a final, gap-filled product with Net Ecosystem Exchange (NEE) partitioned into Gross Primary Productivity (GPP) and Ecosystem Respiration (ER). For more information about the processing levels, see https://github.com/OzFlux/PyFluxPro/wiki. The Samford flux station is situated on an improved (Paspalum dilatum) pasture in the humid subtropical climatic region of coastal south-east Queensland. Located only 20km from the centre of Brisbane city, Samford Valley provides an ideal case study to examine the impact of urbanisation and land use change on ecosystem processes. The valley covers an area of some 82km2 and is drained in the southern regions by the Samford creek, which extends some 13km to Samford Village and into the South Pine River. The Samford Valley is historically a rural area experiencing intense urbanisation, with the population increasing almost 50% in the 10 years to 2006 (Morton Bay Regional Council, 2011). Within the Samford valley study region, the Samford Ecological Research Facility (SERF) not only represents a microcosm of current and historical land uses in the valley, but provides a unique opportunity to intensively study various aspects of ecosystem health in a secure, integrated and long term research capacity. Mean annual minimum and maximum temperatures at a nearby Bureau of Meteorology site are 13.1°C and 25.6°C respectively while average rainfall is 1102mm. For additional site information, see https://www.tern.org.au/tern-observatory/tern-ecosystem-processes/samford-peri-urban-supersite/ .