We present an extension to anisotropic flows of the recently developed Helmholtz and wave–vortex decomposition method for one-dimensional spectra measured along ship or aircraft tracks in Bühler et al. (J. Fluid Mech., vol. 756, 2014, pp. 1007–1026). Here, anisotropy refers to the statistical properties of the underlying flow field, which in the original method was assumed to be homogeneous and isotropic in the horizontal plane. Now, the flow is allowed to have a simple kind of horizontal anisotropy that is chosen in a self-consistent manner and can be deduced from the one-dimensional power spectra of the horizontal velocity fields and their cross-correlation. The key result is that an exact and robust Helmholtz decomposition of the horizontal kinetic energy spectrum can be achieved in this anisotropic flow setting, which then also allows the subsequent wave–vortex decomposition step. The anisotropic method is as easy to use as its isotropic counterpart and it robustly converges back to it if the observed anisotropy tends to zero. As a by-product of our analysis we also found a simple test for statistical correlation between rotational and divergent flow components. The new method is developed theoretically and tested with encouraging results on challenging synthetic data as well as on ocean data from the Gulf Stream.