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Flux measurements over heterogeneous surfaces with growing vegetation and a limited fetch are a difficult task, as measurement heights that are too high or too low above the canopy adversely affect results. The aim of this study is to assess implications from measurement height in regard to low-pass filtering, footprint representativeness, and energy balance closure for a clear-cut site with regrowing vegetation of varying height. For this, measurements from two open-path eddy-covariance systems at different heights are compared over the course of one growing season. Particular attention is paid to low-pass-filtering corrections, for which five different methods are compared. Results indicate significant differences between fluxes from the upper and lower systems, which likely result from footprint differences and an insufficient spectral correction for the lower system. Different low-pass-filtering corrections add an uncertainty of 3.4% (7.0%) to CO
2
fluxes and 1.4% (3.0%) to H
2
O fluxes for the upper (lower) system, also leading to considerable differences in cumulative fluxes. Despite limitations in the analysis, which include the difficulty of applying a footprint model at this study site and the likely influence of advection on the total exchange, the analysis confirms that information about the choice of spectral correction method and measurement-height changes are critical for interpreting data at complex sites.