Different parts of the island have varied origins, some with fresh lavas and spatter cones and others consisting of eroded tuff formations. Baltra Island used to be a US Air Force Base during World War II.

American soldiers in Baltra Island patrolled the nearby waters of the Pacific Ocean, including the entrance to the Panama Canal, for enemy aircraft carriers, warships, and submarines. When the war ended, the facilities in Baltra Island were handed over to the Ecuadorian Government.

Up until 1986, Baltra Island was home to the only airport in the Galapagos Islands. The airport now shares flights to the Galapagos with the San Cristobal Island airport, but it still receives the majority of flights from the mainland. Most cruise operators also start their cruise operations from Baltra Island. Also, because of its proximity to the largest port town in the Galapagos Islands (Puerto Ayora), most tourists who do island-based tours choose to arrive at the airport on Baltra Island.