In the last 6 million years the entire Mediterranean sea dried out and was then refilled repeatedly. (Because the tectonic movements closed and reopened the Strait of Gibraltar. If the Strait of Gibraltar closes and cuts off the the Med from the ocean, the flow of water from the Danube, the Nile and the Rhone is utterly insufficient to compensate for the evaporation and the sea dries out quite promptly.)

@AlexP I thought of this after reading about the Zanclean flood, but ideally I would need a mechanism that could plausibly occur over thousands of years as opposed to millions. Although if we reverse the logic and have tectonic activity occur at the scale of millenia, we could make it work but this is probably worth its own separate question.

I like this question! However, there's a difference between making a lake disappear (Yellowstone-style ebb and flow of underground water and thermal vents) and making an entire ocean disappear. Can you specifically identify the size of the body of water you want to address?

I do not have a specific numerical volume or area I could point to, but it would specifically be a body of water large enough that crossing it without a minimal tech level or goal-setting would be difficult (Oceanian long-range navigators in our own world notwithstanding).

it happens on earth, its called ice ages and glaciation, water gets turned into ice sheets. but it takes a little longer than a millennia. Or are you looking for a local event, then just look at the lakes formed by natural dams. the bridge of the gods forms a new dam ever few thousand years creating a lake.

I am not sure if the resurfaced water body will be the same one that disappeared. It will be entirely different, right?

@Proscionexium For the purpose of my story, what I really need is for the ocean to exist and stop existing as a barrier at various times in the world's history. Whether the water itself is the same is no a priority, but a nice detail

@Qwokker the Mediterranean Sea is pretty small.

@John the oceans receded a measly 400 feet during the last ice age, out of a 12000 foot deep Atlantic Ocean, and 13000 foot deep Pacific Ocean. That's hardly "recede completely".

Oceans are deep. That means there is a lot of water. Narrow your ambition to a relatively small sea like the Mediterranean, which is bottle-necked on two sides.

You specify that it has to be shifted many times in history. How long is your history?

+1 for making me think extreme. At first I was about to say a definite "no way".

@RonJohn my issue is that I really want the ocean as a narrative device that separates civilizations and groups of people at various times, and not at others. I'd abandon the idea of a geologically semi-plausible explanation before I abandon the above idea

@RobertRapplean I'm thinking similar to our world, maybe let's say a Göbekli Tepe kind of deal with human civilizations rising and falling over 10-15,000 years. Except without the on-ramp to industrialization

@RonJohn and that was enough to connect several large islands, including England to the mainland, look up somthing called doggerland. It also connected several continents. the ocean would literally have disappeared for as far as the eye could see. from some locations.

Over what period of time, please?

@John "the ocean would literally have disappeared for as far as the eye could see" is not "large ocean on a planet's surface to recede completely".

Is your story going to be about humans? If you're not locked to human-like beings, I might have an idea.

@RobbieGoodwin I want to write a story that takes place with ellipses over around 10k years or so. Chapters shifting to the vantage point of a civilization in Dry eras, and Liquid eras as they grapple with the changes of there being barriers to other civilizations or not

@Mermaker I am open to many ideas as the story is at a very early stage. Please do not hold back!