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As far as I know, archaeological excavation discovered several layers of the city of Troy, each one built on top of the ruins of the older ones.

I just can imagine how that might have happened.

One possibility: The old ruins are so completely covered by mud or sand that the people building the new city just do not notice them. Or if they notice, they do not care since the old stones deep below ground do not inconvenience them, even when digging cellars.

That might happen once or twice I guess, but several times seems very unlikely to me. How long does it take for a layer of mud or sand to reach the necessary height?

Another possibility: The old city is destroyed or abandoned, but the ruins are still visible above ground. What would new settlers do? Either remove the old stones to get level ground for new buildings, or even use the old stones for the new buildings. Either way, hardly anything would be left of the old city, and very little for archeologists to dig up.

So that seems also unlikely.

What am I missing, how did it actually happen?

EDIT:

Thanks for the link to Formation of underground layers of Rome, that's almost a duplicate I guess, but since my basic problem is not answered there, I'll try to state it more precisely:

The answers so far seem to suggest the following process: The ruins are still visible, but the ground around them has risen several feet. Digging up the old stones would only create a deep hole in the ground which had to be filled again if you want a building on the new ground level: That is considered too much effort, especially if the old stones are considered not very useful as building material anymore (For mud-bricks I get that, but for Roman stones it is harder to understand). So the rubble is levelled into a flat building site and the new building is erected on top of it.

That leaves the following points unclear to me:

1) If the rubble is levelled, can it really form a stable building site? I can only imagine that if the old stones are covered with a layer of earth to form a flat surface. Doing that seems unlikely if the new surface is much higher than the ground around the building.

2) Would levelling the old rubble not destroy most archaeological traces? Why is still so much left to discover?

3) If the earth around the building rises higher and higher over centuries: Why exactly does that happen? Does it happen also outside cities? If only in cities: Is the accumulating dirt brought by wind or river floods? That seems unlikely for cities built on hills. Or is it formed by human waste? How can I imagine that: Garbage heaps beside the streets getting higher and higher and composting into earth that spills over onto the street itself where it is simply trampled down so that the street level rises, and the inhabitants don't care? What if the street is paved?

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    Every city is built on the older version of itself. We excavate in London, and find medieval and Roman layers beneath us all the time. The city doesn't have to be abandoned. People just levelled the site and built on top. – sempaiscuba Apr 27 at 18:11
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    If you want some really interesting info on building in layers, look into Çatalhöyük – justCal Apr 27 at 19:23
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    Long story short: the old city is literally covered by the trash left by the previous generations. Archaeologists spend most of their time rummaging through age old trash to see if they get interesting things (often pottery shards, but sometimes other stuff). You can say a lot about a person by looking at their trash :). – Denis Nardin Apr 28 at 6:26
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I'm not sure if it's accepted to cite another stackexchange answer, but this one by MAGolding seems to be your solution. Formation of underground layers of Rome

I suspect the reality is closer to your second possibility. As other answers here have already said, people would reuse the materials from older buildings to save costs, but lots would be unsalvageable. Most of the material that fills in the "old" city comes from mud bricks, which disintegrate much faster than masonry, and probably faster than soil would naturally accumulate as well. The mound that builds up over time that serves as the foundation of the next city is called a Tell in archeology. https://en.wikipedia.org/wiki/Tell_(archaeology) This happened gradually for the most part, so some of the "layers" of city overlap considerably.

As for how long it would take for one "layer" to be covered up, I haven't seen any figures more specific than "generations to centuries." Keep in mind though that Troy had been the site of a major city for about 1500 years already during Homer's time.

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    How long it takes is probably subject to lots of different factors; weather, building materials, what kinds of trash the society produces, height of the water table, what kinds of rodents/insects make burrows. – Ryan_L Apr 27 at 23:39
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One possibility: The old ruins are so completely covered by mud or sand that the people building the new city just do not notice them. Or if they notice, they do not care since the old stones deep below ground do not inconvenience them, even when digging cellars.

There's some of both. Basically, besides the accumulation of mud, trash, and what have you, they cared so little about what lied beneath that they'd reuse the stones to cut costs. It's for this reason that scores of historical monuments no longer exist.

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And another possibility: old buildings are torn down to form the foundation for new buildings. It's not impossible for one city to be disbanded, turn into rubble and be occupied again. But that would be unusually strange in many cities. Yet that is what we see in most older permanently occupied cities: many layers of rubble. Surely Paris, London and Rome weren't abandoned many times?

Occam's razor works fine for me: the cities weren't abandoned, they used the rubble of old building(s) to build new ones on top.

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    Especially if those buildings were using mud bricks like many structures in Troy. – sempaiscuba Apr 28 at 0:46
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I think this paragraph from Georges Roux's Ancient Iraq might be enlightening. He talks specifically about the houses in ancient Mesopotamia, but I'd be surprised if most of it did not apply almost till the beginning of the modern Age (From Chapter 2, section 1: The buried cities of Iraq):

Every summer it was necessary to put a new layer of clay on the roof in anticipation of the winter rains, and every now and then the floors had to be raised. The reason for this was that rubbish in antiquity was not collected for disposal but simply thrown into the street, so that the street level gradually rose higher than the floor level of the houses that bordered it, allowing the rain and the filth to seep in. Earth was therefore brought into the rooms, rammed over the old floors and covered with another coat of plaster. It is not infrequent for archaeologists to find two, three or more superimposed floors in one house. Provided these things were done, mud-brick buildings could last for a great many years. But then one day something happened. Whether it was war, fire, epidemic, earthquake, flood or change in river course, the result was the same: the town was partly or totally deserted. The roofs left unattended collapsed and the walls, now exposed to weather on both faces, crumbled down, filling up the rooms and sealing off the objects left behind by the householders. [...]

After years or even centuries of abandonment, new settlers would perhaps reoccupy the site, attracted by such things as its strategically or commercially advantageous position, the abundance of its water supplies or, possibly, a lingering devotion to the god under whose aegis it had been built. Since they had no means of removing the enormous mass of debris, they levelled off the ruined walls and used them as foundations for their own building. This process was repeated several times in the course of years, and as ‘occupation levels’ succeeded one another the city gradually rose above the surrounding plain.

So it seems that it was a combination of two factors: the trash thrown into the ground by the inhabitants would periodically force them to build a new floor above it (yeah, it does sound weird to modern ears), and when disaster struck the new occupants typically leveled the heaps of rubble to form the foundations for their new city.

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