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Cologne comes to my mind, it was abandoned after WW2 and left to the mutations caused by Allied bombs.
 
Many cities in Europe that were prominent in the Roman era either no longer exist, or were totally destroyed and then later on some other city was founded on or near the original site.

Could you give me some examples?

And as per the OP and Henry IX's post, if a city is rebuilt on the same spot after being razed, I would count that as continuous habitation and as the same city. Sometime between Acquincum and Budapest, the area might have deteriorated to merely a village, but the area was in continuous habitation since the Romans, and very likely since well before them.
 
Arent there many abandoned/lost cities in Egypt like Chepesh ?
 
What about the Maya old cities in America (the continent), or the very Teotihuacán?
 
Could you give me some examples?

And as per the OP and Henry IX's post, if a city is rebuilt on the same spot after being razed, I would count that as continuous habitation and as the same city. Sometime between Acquincum and Budapest, the area might have deteriorated to merely a village, but the area was in continuous habitation since the Romans, and very likely since well before them.

Some examples:
  • Carnuntum (Austria).
  • Aquilea (Italy).
  • Ostia (Italy).
  • Italica (Spain).
  • Recopolis (Spain).
  • Clunia (Spain).
  • Segobriga (Spain).
  • Mentesa (Spain).
 
Could you give me some examples?

And as per the OP and Henry IX's post, if a city is rebuilt on the same spot after being razed, I would count that as continuous habitation and as the same city. Sometime between Acquincum and Budapest, the area might have deteriorated to merely a village, but the area was in continuous habitation since the Romans, and very likely since well before them.

Note that the city was razed once more in 1241 by the Mongols and the new city/castle was built on a more defensible terrain and the name transferred to the new city. The district where Aquincum is is called Old Buda.
 
There are a bunch of towns in Scotland and Northern Ireland that were once built on coastal sites. As the coast rebounded from glaciation and sea leaves simultaneously rose some of them wound up landlocked and wasted away, and others wound up swallowed by the sea and this abandoned. Numerous sites in what is now the North Sea were abandoned when the region known as doggerland was submerged. A variety of coastal sites in France and Northern Italy that were once constructed at natural harbors were abandoned when they silted up due to changes in river courses or advancement of river deltas. In Ancient Greece a number of city sites got abandoned when changes in trade patterns or political boundaries or technology rendered them no longer useful. For example a set of boat skids and portage roads to portage across the thinnest point connecting the Mycenaean peninsula was a key strategic point with considerable cities at both ends. Then a rise in size of merchant ships, and increase in using wind instead of oats for their propulsion rendered the ‘shortcut’ not useful.
 
There are a bunch of towns in Scotland and Northern Ireland that were once built on coastal sites. As the coast rebounded from glaciation and sea leaves simultaneously rose some of them wound up landlocked and wasted away, and others wound up swallowed by the sea and this abandoned. Numerous sites in what is now the North Sea were abandoned when the region known as doggerland was submerged. A variety of coastal sites in France and Northern Italy that were once constructed at natural harbors were abandoned when they silted up due to changes in river courses or advancement of river deltas. In Ancient Greece a number of city sites got abandoned when changes in trade patterns or political boundaries or technology rendered them no longer useful. For example a set of boat skids and portage roads to portage across the thinnest point connecting the Mycenaean peninsula was a key strategic point with considerable cities at both ends. Then a rise in size of merchant ships, and increase in using wind instead of oats for their propulsion rendered the ‘shortcut’ not useful.
Similarly all along the East Yorkshire coast there have been towns and settlements that were lost to coastal erosion. Even very big ones like Ravenser Odd.
 
Cologne comes to my mind, it was abandoned after WW2 and left to the mutations caused by Allied bombs.
My family is duty-bound to the 16th generation to patrol the borders of the Rhineland and send any of those abominations back to whatever 'car-nie-wall' is.

Also, IIRC, there are now a number of villages in the Eastern Bundesländer who are either completly or effectivly abandoned.
 
There are a bunch of towns in Scotland and Northern Ireland that were once built on coastal sites. As the coast rebounded from glaciation and sea leaves simultaneously rose some of them wound up landlocked and wasted away, and others wound up swallowed by the sea and this abandoned.

Kenfig in south Wales is a coastal one that ended up buried by deposition of sand.
 
Pompey wasn't rebuilt after it was buried by volcanic ash.

A new city was built across the river from the ruins of Nineveh, but it seems like the old site is still mostly deserted from what I've read, except when it's being used by terrorists or for illegal activities.

As pointed out, Acquincum was abandoned, and either new sites were built nearby, or possibly the old suburbs became the new center. The reasons for its original existence were still valid, so it was replaced, even though it wasn't rebuilt. The same happened with Carthage, where a new city was built nearby, because the underlying reasons for settling in the area were still valid. The old sites remained mostly or entirely abandoned, despite the flourishing of the new cities nearby.
 
Reading through @Semper Victor's excellent Sassanian thread, I was stuck by the frequent mention of cities which had been wholly abandoned by ~1000 CE, never to be refounded.

However, a cursory google search reveals that wholly abandoned cities are extremely uncommon in Europe, and are only a thing in the US because they were single-resource boom towns, which never diversified.

How common was if, in the timeframe of lets say 476-2018, for a city (not a village) to be abandoned and never rebuilt, refunded? Is my impression that this is very common in the ME correct, and why?
Rainfall.

In Europe, when the river shifts, it's still raining and you can still have a settlement. Hence, the city isn't abandoned, even if it becomes less important.

In the orient, there is not so much rain. When the river moves, so do all the people.

Nothing magic about it.
 
That's not how bacteria or disease usually works, so your suspicion is likely way off.

Some pathogens can survive outside a host body for remarkable amount of time, with anthrax being a good example. You are correct that it isn't very common, however, and I personally believe that it would only have been minor settlements that were abandoned for such reasons.
 
Some pathogens can survive outside a host body for remarkable amount of time, with anthrax being a good example. You are correct that it isn't very common, however, and I personally believe that it would only have been minor settlements that were abandoned for such reasons.

Some bacteria in water sources could also effectively continue infecting an area after human abandonment. Cholera for instance.
 
Also, not quite cities, but at least in scandinavia plenty of farmsteads/small villages were never resettled after the Black Death. (by the point the population had recovered, there were alternative places to go and things to do rather than trying to make something of these mariginal lands)
 
If we understand abandonded as all meaningful economic activity ceasing and the population dwindling with no natural increase I would argue a few examples: Gamla Uppsala, Birka.
I would also move that many Towns (Tun, Köpingar) should be understood as disappeared as their formative and main economic activity ceased and while a town or village exists in the same spot it is not the same village or town that existed before. Köpingsvik, Uppåkra, Berga for example.
Arguably places like Harg and Gamleby were indeed abandonded, Harg being a works village but Gamleby being an actual town which saw no economic progress until 400-years after its forced evacuation (that story has 7 twists to it though.)

Same goes for former trade emporia on southern (Wendish) coast of the Baltic Sea. There are estimates that Wolin and Hel could have as much as 10 thousand inhabitants each at around 1000, which is insane for Viking Age. Both were abandoned in 1100s to 1200s. Wolin's harbour got silted, while Hel was slowly flooded. Modern Wolin and Hel were refounded later as much smaller settlements in some distance from the cities' original locations.
 
The Netherlands has at least a ~100 abandoned villages and towns:

https://en.wikipedia.org/wiki/List_of_settlements_lost_to_floods_in_the_Netherlands

One interesting example was the city of Reimerswaal, which was abandoned due to a combination of politics and natural disasters. It had a seat in the states of Zeeland, but choose the Catholic side in the Dutch independence war. It was subsequently burned down by the Protestant side, and it gained less resources after the war to rebuild defenses against the water. After a few floods it was permanently abandoned.