Leaf litter accumulates and breaks down and becomes new soil, mountains and hills erode and that sediment accumulates in lower areas, wind move lots of sand and fine sediment around, All of that piles up in places until things once on top of the soil are now buried.

It's a little more complicated than that, but that's part of the process.

Another aspect is that cities used to literally rise as they deposited waste in situ and had to build up as 1st floors became basements. This is partially the source of mounds.

Neat reddit discussion: https://www.reddit.com/r/AskHistorians/comments/17je7i/arche...