It's almost certainly the first episode of Storm, drawn by great Don Lawrence. Here's the summary:
Storm was an astronaut on Earth. One day a red spot was detected on the surface of Jupiter and Storm was send to investigate it, but something went wrong and he got sucked into the red spot, which transported him through time. Storm returned to Earth to discover that it was no longer the planet he had left - over a thousand years had gone by, and the world had descended into barbarism. There is nothing anymore that he recalls from the past. He is in a strange world without oceans and seas. It is as if the prehistoric has returned. Primitive peoples, bizarre and exotic animals have dominion over the Earth.
Storm is captured by barbarians and brought to a city located at what was once the bottom of the Pacific ("the deep world"), ruled by the tyrant Ghast. In prison he meets Ember and Kiley, freedom fighters who opposed Ghast. Together they escape, chased by Ghast, to an underground power station, Mandros, run by a hologram. He tells Storm that the natural world has changed and why the oceans and seas are gone. Ghast, however, has followed them. He destroys the central computer, which causes all the water of the oceans and seas, contained subterraneanly, to be pumped back to the surface with disastrous consequences. The deep world again fills with water, causing everyone on Earth to seek shelter from the raging waters. Storm and Ember survive, escaping on a raft, and go on to further adventures together, eventually discovering a time machine that takes them across the multiverse.