Tower- and aircraft-based flux measuring systems provide temporal as well as spatial information on the mass and energy exchange associated with complex ecosystems. This presentation will show how the data from this combination of measuring systems can be used to obtain area averages fluxes for as complex an ecosystem as the boreal forest. A cover type - unmixing method was developed to calculate the flux density for several underlying cover types. This method uses a linear inversion technique with the footprint-weighted cover type fractions as the set of coefficients for each segment of a flight line for which a flux value is available. It will be shown that when simultaneous tower-based flux measurements in the dominant cover type are used as a constraint, then realistic flux estimates from cover types without tower measurements can be obtained. The information from one tower and for all these cover types can then be used to obtain area average flux estimates.