The objective of this paper is to evaluate the baroclinic and barotropic components of sea surface height (SSH) anomalies in the Southern Ocean and investigates the causes for the weak correlation between hydrographically derived and satellite measured SSH anomalies. To this end, data obtained by six Pressure Inverted Echo Sounders (PIES) deployed south of Africa were used to derive baroclinic and barotropic SSH anomalies. Our results show that the barotropic component accounts for 30%–60% of the variability between the jets of the Antarctic Circumpolar Current (ACC). In contrast, the jets associated with the major ACC fronts are predominantly baroclinic. The deep baroclinic component is important in the ACC and accounts for the major part of the baroclinic variability. The comparison with along-track satellite altimetry (Jason 1/2) shows correlations coefficients of 0.24–0.92, with low values in regions of high-barotropic variability. The comparison with gridded Aviso satellite altimetry generally shows higher correlation coefficients (0.33–0.92) and lower root mean square (RMS) errors compared to the along-track product. In conclusion the barotropic SSH anomaly plays a major role in this region and has to be accounted for when assimilating SSH into ocean models. Due to their high-baroclinic component, the correct representation of the time and space varying ACC fronts seems to be crucial for the right SSH anomaly partitioning used for assimilation purposes. Gridded products, namely Aviso, seems to be more suitable compared to along-track products (Jason 1/2) in representing the variability of SSH anomalies.