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I have a bay of water containing several Krakens. One day, due to the efforts of a magical organization, all of the water disappears. The Kraken fall and die on the bed of salt that is left behind. Each are about 50 meters in length.

Assuming the Kraken are preserved by the salt, how long could their carcasses survive intact, before they rot away and only the bones are left? My plot calls for them to survive a bit more than two millennia, but I'm not sure if this is realistic.

I'm going to assume that when you say "Kraken" you mean "giant octopus monster" meaning something biochemically identical to a modern octopus but huge. I'm also assuming that the water stays gone and the environment is perpetually dry. Given those assumptions the real world example of seal carcasses in Antarctica's Dry Valleys should be educational. Those bodies are preserved by the dryness of the environment more than the chemical action of the salt in the air but both play a part, they remain relatively intact (as in you can still tell it's a seal) for at least as much as 2600 years, so your two millennia shouldn't be an implausible time period.

Note that the only "bone" in a traditional Kraken would be the beak, possibly sucker hooks as well if they take more after giant squid.

Preserving organic materials or organisms in salt requires more than just laying on top of a salty layer.

It requires complete coverage with salt and frequent renewal of the salt, to remove the salt saturated with the water extracted from the organism.

Considering that your Kraken, whatever it is made of, is 50 meters long, I think only a very minor part of its body would be in contact with salt.

Decomposition of the body would then be unavoidable.

If you want to preserve the bodies in salt, they should have parts with low water content (if you dehydrate a jellyfish you will end up with nothing). A Kraken, being often depicted as a sort of cephalopod, has practically no hard parts.

If you handwave this and somehow manage to properly prepare the body in salt (and I assume a magical organization capable of emptying a bay can also manage to stir some Krakens in salt) by completely covering it in salt, your best bet is to cover the whole volume with non permeable materials, like clay. If layers of clay preserved rock salt in the bottom of the sea, they can presumably protect your salted Krakens for a couple of millenia.

If "all of the water disappears" includes the water in the krakens and you could keep the bay dry, then you would likely end up with some shriveled kraken mummies that could easily last a couple thousand years.

Mummification works best on desiccated corpses that are left in dry areas, which describes the krakens and your former bay perfectly. As you expected, salt would help preserve them by leeching extra moisture out from the carcasses. However, the key is keeping the bay dry: unless the wizards also dam up the entrance to the bay and ensure that it doesn't fill with rain water or humid air, then no amount of salt would help them and they would quickly rot.

As a side note, if you wanted some natural kraken salt statues then the magical organization can regularly let water seep into the bay/krakens before removing it again. This cycle of seeping/evaporation will fill the kraken's cells with salt in a process called permineralization, the end result being petrified kraken corpses made entirely of salt with little to no organic material remaining.

Do you need to dry out the area? If it's about preservation of the carcasses maybe you could do other things to preserve them:

You could turn the water in the bay super salty and turn their carcasses into salt, and maybe then remove the water after (or just not at all) ?
https://www.livescience.com/55904-crystal-bride-gown-photos.html

Also as mentioned before it could still rain which could possibly spoil the carcass, would it be possible to freeze the bay instead?

Sorry if this feedback was not welcome, but I just wanted to throw this out there.