Successive multibeam echo sounder surveys in tidal channels off Esbjerg (Denmark) on the North Sea coast reveal the dynamics of subaquatic compound dunes. Mainly driven by tidal currents, dune structures show complex migration patterns in all temporal and spatial scales. Common methods for the analysis of bedform migration are based on the description of average characteristics as dune length, height and celerity. Their application to superimposed structures is dissatisfying as the recognition of dunes is subjective and work intensive. The high resolution and accuracy of the bathymetric surveys allows the application of a procedure, which has been a standard for the analysis of water waves for long times: The bathymetric signal of a cross-section of subaquatic compound dunes is approximated by the sum of a set of harmonic functions, derived by Fourier transformation. If the wavelength of the single harmonic constituents is assumed to be uniform and stationary, bedform dynamics can be completely assessed by changes in amplitude and phase. Dune migration at several transects were analysed and quantified by taking into account the phase differences of individual harmonic constituents. An assessment of bedform migration was achieved, as the growth and displacement of every single constituent can be distinguished. It can be shown that the changes in amplitude remain small for all harmonic constituents, whereas the phase shifts differ significantly. Thus the harmonics can be classified into components of different celerity. The separate re-composition of harmonic constituents with zero or low phase shifts sums up to what can be regarded as the stable part of the original signal. On the other hand the summation of constituents with high phase differences forms the purely kinematic signal. The proposed method overcomes the above mentioned problems of common descriptive analysis as it is an objective and straightforward mathematical process. The spectral decomposition of superimposed dunes allows a detailed description and analysis of dune patterns and migration.