The dunes are also now separated at the southern end by agricultural land from the much more extensive Gran Desierto de Altar, to which they once were linked as an extreme peripheral "finger".

The prevailing westerly and northwesterly winds carried the sand eastward from the old lake shore to their present location which continues to migrate southeast by approximately one foot per year.

During World War II, the U.S. military conducted desert warfare training on the dunes, which were part of the California-Arizona Maneuver Area.

[6] Research indicates that there is significant reduction in the diversity and abundance of species in dune areas subject to heavy ORV traffic.

[8] As they are the largest dune ecosystem in the United States, there are many species which are endemic to the Algodones system, so the region overall is biologically unique on a global scale.

The Algodones were once part of an even greater dune system that now resides primarily in the Mexican state of Sonora, with a few extensions also in southwestern Arizona, especially in the vicinity of Yuma.

Accordingly, it is likely that many of the species presently known only from the Algodones also occur in the Gran Desierto de Altar in Mexico, but this is difficult to ascertain without biological surveys of the latter area.

Outside of movies, the dunes also appear in the opening sequence of the TV series Kung Fu, and were the filming location for the music video of Deftones' 2003 single Minerva.

According to the United States Department of Agriculture, the Plant Hardiness zone is 10a with an average annual extreme minimum temperature of 32.7 °F (0.4 °C).