When I was much younger, I remember reading a story titled “And the Waters Prevailed”, about humans at the time of the filling of the Mediterranean basin. I’m going to check my library’s catalogue and maybe read it again.
Julian May’s Saga of Pliocene Exile series had the opening of Gibraltar and flooding of the Mediterranean as a major plot point.
I looked that up; it was by Daniel Moreau Berringer. Never read it, but I might.