Sometime around 1920, an unnamed oceanographer stumbled upon some of the ruins of an Atlantean laboratory.  He studied it for years, eventually using the biotechnology he adopted from  the ruins to conduct experiments on his young son, allow him to survive underwater and engage in feats of great strength and speed. He also educated his son extensive on the zoology of the ocean, allowing him to communicate, if not command, a variety of different kinds of sea life.  The fate of the oceanographer is unknown.  The son grew up to become the hero known as Aquaman (More Fun Comics #73).

The first known encounter with the descendants of Atlantis in modern history occurred in 1940 when the Ophirean regent Setap contacted Zatara the magician, claiming to have a map to the ancient realm of Atlantis.  Chartering a boat, the two sailed into the middle of the Atlantic and Zatara was lowered to the sea floor in a bathysphere. There he indeed found an outpost of ancient Atlantis, guarded by underworld species of humanoids and sea serpents.  Evading them, he meets Gath, the leaders of this colony of Atlanteans and learns much of the continent’s history.   As he communes with the Atlantean, Setap is accosted by one of the sailors, Barnacle Will, who sees the prospect of Atlantean gold too enticing to resist.  The group converge on the colony and disturb Roor, an ancient mystical octopus who is a sworn for of Atlantis.  Roor kills Barnacle Will but is eventually defeated by Zatara, who departs the Atlantean colony while Setap chooses to remain (Action #18).  No further record of this colony exists. 

In August of 1940, the Book of Thoth was found by an unnamed wizard, who used its spells to fleece wealthy men in London before being stopped by Doctor Fate.  Rather than risk it’s re-discovery, Fate reduced the book to dust and scattered the dust into the sea. Whether that was the end of it is unrevealed (More Fun #58). 

In 1942, Zatara encountered another colony of former Atlanteans off the coast of Florida.  This group had developed an underwater city, though the lacked the ability to breathe underwater unaided.  This city recaptured much of the architecture of the original Atlantis and was ruled by Nargo, an evolved mutant Atlantean with enormous mental powers housed in a larger than normal brain.  The aging Nargo followed affairs in the surface world and identified a surgeon who could help him resolve a condition that was killing him.  Kidnapping sailors as ransom, Nargo convinced the surgeon to come but Zatara also tagged along.  After eventually overcoming Zatara, the surgical anesthesia allowed Zatara to gain the upper hand and in the battle for supremacy, the city was destroyed and Nargo seemingly killed in the process.  Nothing more of this colony is known (Action Comics #47). 

In 1943, Batman and Robin were investigating the disappearance of ships in the North Atlantic and found a whirlpool that pulled them into another underwater colony of Atlantis. Ruled by Emperor Taro and Empress Lanya, the government of the colony has been deceived by Nazi Admiral Von Buritz into believing that the Nazis are in a righteous war against the Allies.  The whirlpool is how the colony refreshes its air supply and the Nazis were using the outpost as a military base and the whirlpool to damage ships.  Batman and Robin reveal the Nazis are the true aggressors and obtain guarantees of protection of ships from the whirlpool from the Atlanteans (Batman #19). Whether this remained the case and whether the Nazis used this knowledge of Atlantis further has not been revealed.