Wouldn't it then be very easy to prove that part of the earths crust was indeed under water at some point, other than just seashell fossils?
Sure it would be! That's what the geologists in England showed, quite conclusively, by about 1840. Based on the types of rocks, as well as fossils, they showed beyond reasonable doubt that England had been seafloor on several occasions, for huge periods of time, and that parts had been dry land at various times, too. The geologists since 1840 have been busy showing the same thing for most of the rest of Earth's surface: the top of Mt Everest, for instance, is made up of skeletal remains of sea critters that were compacted to limestone, buried tens of thousands of feet deep where it was hot enough to convert the limestone partially to marble, and then uplifted and the covering rocks eroded off to leave the tallest peak we have this millenium.
Same sort of thing under my chair: there's a reef down there 6500 feet that grew in the Permian. It's covered up in rocks that formed in shallow seas that dried up on occasion - there's salt and gypsum beds to prove it. And I'm 500 miles from the ocean now, and 2700 feet above it.