Measurements of regional net ecosystem exchange (NEE) were made over a period of 21 days in summer 2002 in the South-Central part of the Netherlands and extrapolated to an area of 13 000 km2 using a combination of flux measurements made by a Sky Arrow ERA research aircraft, half-hourly eddy covariance data from four towers, half-hourly weather data recorded by three weather stations and detailed information on regional land use. The combination of this type of information allowed to estimate the net contribution of the terrestrial ecosystems to the overall regional carbon flux and to map dynamically the temporal and spatial variability of the fluxes. A regional carbon budget was calculated for the study period and the contributions of the different land uses to the overall regional flux, were assessed. Ecosystems were, overall, a small source of carbon to the atmosphere equivalent to to 0.23±0.025 g C m−2 day−1. When considered separately, arable and grasslands were a source of, respectively, 0.68±0.022 and 1.28±0.026 g C m−2 day−1. Evergreen and deciduous forests were instead a sink of −1.42±0.015 g C m−2 day−1. During the study period, forests offset approximately 3.5% of anthropogenic carbon emission estimates obtained from inventory data. Lacking of a robust validation, NEE values obtained with this method were compared with independent state of art estimates of the regional carbon balance that were obtained by applying a semi-empirical model of NEE driven by MODIS satellite fAPAR data. The comparison showed an acceptable matching for the carbon balance of forest that was a sink in both cases, while a much larger difference for arable and grassland was found. Those ecosystems were a sink for satellite-based estimates while they were a source for the combined aircraft and tower estimates. Possible causes of such differences are discussed and partly addressed. The importance of new methods for determining carbon balance at the regional scale, is outlined.