Lenticular sand bodies in the Upper Jurassic Norphlet Sandstone in the northeastern Gulf of Mexico basin have been interpreted as preserved large linear dunes that subsided into the underlying Louann Salt layer. Due to imaging difficulties, the thickness of the underlying salt is largely unknown. We performed physical experiments and created a mathematical model to understand dune and salt deformation and to determine the controls on the final preserved dune topography. Nonuniform dune geometry results in unequal loading by sand that drives locally varying subsidence into the salt substrate, resulting in varying degrees of dune flattening and dune relief. Our results indicate that initial salt thickness relative to dune size governs the initial rate of subsidence, thus affecting the final dune topography. However, interdune spacing and dune geometry are also important because they set the pressure gradient and determine the maximum possible subsidence. We conclude that preserved dunes with high relief indicate areas of relatively thin salt thickness and/or close dune spacing, and that dunes with low relief indicate areas of relatively thick salt thickness and/or wide dune spacing. For the case of the Norphlet Formation, dune spacing and salt thickness likely played the major roles in controlling dune subsidence.