But sometimes we do uncover fossils in an archaeological context. In the case reported here, marine fossils seem to have been used in a religious context at Palenque. The Maya of the Late Classic period apparently knew that they had uncovered the remains of long dead sea creatures.
However, I would not be so quick to conclude that finding those fossils caused the Maya to believe that the world was originally covered with water. A primordial ocean is such a widespread element in mythology that I find it far more likely the fossils merely reinforced an existing cosmogony. It will be interesting to see what further research will turn up.