Sedimentary rocks from Virginia through Florida record marine flooding during the mid-Pliocene. Several wave-cut scarps that at the time of deposition would have been horizontal are now draped over a warped surface with a maximum variation of 60 meters. We modeled dynamic topography by using mantle convection simulations that predict the amplitude and broad spatial distribution of this distortion. The results imply that dynamic topography and, to a lesser extent, glacial isostatic adjustment account for the current architecture of the coastal plain and proximal shelf. This confounds attempts to use regional stratigraphic relations as references for longer-term sea-level determinations. Inferences of Pliocene global sea-level heights or stability of Antarctic ice sheets therefore cannot be deciphered in the absence of an appropriate mantle dynamic reference frame.