Abstract The Surface Water and Ocean Topography (SWOT) observatory is a complex system and contains unique systematic errors not in historical nadir altimeter observations. The errors contain expected shapes in the cross‐track direction, and functional coefficients describing the shapes are correlated in the along‐track direction. Existing nadir altimeter observations enable comparison to the SWOT observations. In the approach here, the SWOT error power spectral density in the along‐track direction indicates the SWOT residual systematic errors are larger than nadir observed signal down to scales of 1,430 km in the PIC data and 2,500 km in the PGC data. The results guide considerations in SWOT processing and error removal.