During operation for the USSB the ship suffered serious damage in a grounding on the coast of Brazil, and later, operating for Clinchfield Navigation, was involved in a collision with a tug in Havana, Cuba, resulting in the tug being sunk. She and a crew of thirty-two vanished in December 1925, while en route from Charleston, South Carolina, to Havana, with a cargo of coal.

The wreck was discovered in the 1980s, but not identified until January 2020.

Cotopaxi was one of three of the seventeen Design 1060 ships built at the River Rouge Yard lost and initially listed as missing.

Coushatta (hull 216, ON 217728), renamed John Tracy, was listed as missing on a voyage from Norfolk, Virginia, to Boston, January 1927. The ship is now listed among the collier wrecks of Stellwagen Bank National Marine Sanctuary where ships with coal cargoes are second only to fishing vessels as victims of disaster.

Coverun (hull 221, ON 218005), after being renamed Mahukona, and then sold and operating as Santa Clara, under the Brazilian flag, was listed as missing southwest of Bermuda, February 1941, while on a voyage from Newport News to Rio de Janeiro.

Several were lost due to wartime action, with others lost to other causes. Corydon (hull 206, ON 217236) foundered in the Bahama Channel during a hurricane in September 1919. Cottonwood (hull 211, ON 217423), renamed Stanburn, foundered October 1946, after striking a submerged object.

One of the ships, Covena (hull 220, ON 217810), became notable as the unique U.S. Army Port Repair ship Junior N. Van Noy. That ship was first of the port repair ships to sail for Europe where it engaged in repairs at Cherbourg, France.

In the 1977 film Close Encounters of the Third Kind, Cotopaxi is connected to the legend of the Bermuda Triangle, and is discovered in the Gobi Desert, presumably set there by extraterrestrial forces.