The origin of the GSD has been debated for more than a century. More recent publications identify the flood plain of the Rio Grande as the sand source. Although most publications do not assign dates to the dune formation, a few infer that the process began about 12 ka and link it to increased discharge and sedimentation during deglaciation of the San Juan Mountains. The physical evidence, however, indicates that the floor of the closed basin north of the Rio Grande, not the river flood plain, was the primary source for the GSD and adjacent inactive dunes—which are more than ten times as extensive as the GSD.

Although the topography of the west flank of the Sangre de Cristo Mountains influenced the location and height of the GSD, it did not restrict sand deposition to this area. Eolian sand blankets the east edge of the San Luis Valley for ~30 km north of the GSD and for ~35 km to the south, dimensions nearly coincident with the length of the closed basin. The parabolic dunes north of the GSD indicate a sand source and transport direction unrelated to the Rio Grande. Also, dune belts typically flank the lee side of rivers known to be the source of eolian sand; dunes are conspicuously absent along the lee side of the Rio Grande. In addition, the coarse texture and poor sorting of Rio Grande alluvium make it an unlikely source for large dunes. Finally, the timing inferred for onset of sand transport and dune formation seems improbable. Archeological, paleontological, and stratigraphic data indicate that at the end of the Pleistocene, lakes, marshes, and denser vegetation than exists today occupied the area between the Rio Grande and the GSD. These conditions would have retarded wind erosion.

Stratigraphic evidence and numerical ages show that water table fluctuated repeatedly during the Holocene and, presumably, for much of the Pleistocene. During times of greater effective moisture, water table rose and shallow lakes formed on the basin floor. During megadroughts, water table fell and exposed sandy lake-floor sediment to wind erosion. Thus, lakebeds on the basin floor episodically contributed new sand to a growing dune system. Between megadroughts the sand supply was replenished by inflow from San Luis Creek and its tributaries, which drain the northern San Luis Valley.