There’s a lot of ways we can figure out ancient sea level. There’s three main ways and they are so the sized together to try and get a complete picture. two methods both come from ocean sediment cores. Using sediment codes you can do two things. Depending on the kind of sediment you find and how old it is, you can reconstruct ancient shorelines. There are usually big sediment deposits that get left behind when sea level dramatically shifts up or down, and these are nice indicators of an ancient shoreline. Sediment cores can also be used to estimate global sea level using oxygen isotopes. Oxygen isotopes fractionate due to natural processes in the water cycle, so depending on the ratio of oxygen 18 to 16, we can take a guess at how much ice was on the land surface. Since we assume the global amount of water is somewhat constant, if we know how much is locked up on land then we can calculate how much must have filled those ocean. Combined with geological models of ancient continent shapes you can arrive at a global sea level. You can also use biostratigraphy like u/agate_ said. Corals are great for this because they live in colonies that can be tens of thousands of years old, so they allow us to see for slight changes in depth and ocean chemistry in the relatively recent past.

Also no denying historic sea level is not equivalent to a flat earther. The major reason to me is that whenever we talk about the past in science we have to put huge asterisks next to everything. We can’t ever really be certain something that happened thousands to millions of years ago happened as we think it did. However we can observe the earth as it is right now, and thus that it isn’t flat.