Most geologists believe the basin where the Salton Sea is now located was never part of the Gulf of California / Sea of Cortez and was actually far above sea level in the distant past. Geological evidence strongly indicates that it was tectonic movement through the ages that caused the region to subside hundreds of feet below sea level and create the basin the Salton Sea now occupies.
Animation of Tectonic Plate Movement
This animation demonstrates the tectonic plate movement that created the California Baja Peninsula, Gulf of California / Sea of Cortez, and the region that would one day become the Salton Sea.
