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Convective boundary layer (CBL) budgetting is regarded as a technique with the potential to estimate regionally integrated surface fluxes of trace gases, sensible and latent heat. We present two practical approaches to this technique and apply them to the experimental data, collected by flying vertical profiles over non-homogeneous terrain consisting mainly of beech forest and agricultural fields. Both approaches are quasi-one-dimensional. The first is to evaluate the budget for an air column whose top is set to CBL height and thus varies considerably in the course of a day. The second, presented here for the first time, evaluates the budget for an air column of fixed mass. We show that the latter approach requires fewer assumptions than the former, while producing results of at least comparable, and often better, accuracy. Error estimates typically yield 10–20% for fluxes of CO2 and sensible heat, and 20–30% for latent heat. These estimates, however, do not include the uncertainty due to horizontal advection. We address this issue by showing how profile information above the CBL top can be exploited to estimate bounds for large-scale advection within the CBL. We test this idea on our data, with the ambiguous result that on some occasions the obtained bounds place realistic constraints on the magnitude of the advection, while on others they are too wide to be useful.