Rim Pool

The main chamber in ATM where most artifacts are located is completely dry (other than seepage from the roof) and has been for a long time.  I also suspect the chamber was dry when the Maya used it.  However, at some point in between, there was a lot of water flowing through the chamber, and this water built rim pools and calcified many artifacts.  

I asked Francisco about this, and did not get much of an answer.  My suspicion is that at some point, probably due to volcanic or seismic activity there were floods of water that left large amounts of sediment in normally dry areas, which eventually solidified as these areas dried out. In this photo, you can see the partially covered skull and pots, and to my eye it looks like they were covered in sediment which then hardened.