There are a couple of things at play here.
One, we have that pretty cool-looking map of Athas that some guy made in the early 2000s/late 90s, that shows the entire planet covered in silt, and the Deadlands covering a sizable portion of the planet as well. You surely know the one I’m talking about, and I think it’s heavily influenced a LOT of dark sun players.
Second, there’s the athas.org team’s decision to blame the silt sea on Keltis casting an out-of-control epic spell to mess with some lizard folk, which resulted in the seas literally turning into silt.
Third, there’s the very clear implication that the Crimson Savanna of the Kreen Empire is actually the former ocean floor, with the Jagged Cliffs being the edge of a continental shelf.
Fourth, there’s the fact that the silt sea as it “currently” exists postdates the cleansing wars’ conclusion (Giustenal at the time of Dregoth’s assassination was still a port city on the shores of the Sunrise Sea).
Fifth, Borys is clearly blamed in multiple sources for the rapid degradation of Athas during his “century” of madness.
Sixth, Marnita is explicitly said to be the “last sea” of Athas (even though it totally doesn’t make sense as it’s barely more than a large lake, is well above the “sea floor” level of the Crimson Savanna [which, by the way, Kosveret is said to be an elf from the Crimson Savanna during the Green Age, which doesn’t make a lot of sense, but I always chalk that up to a lot of inconsistencies and lack of communication between TSR writers], and there isn’t any clear and plausible way that it could once have been a part of the oceans/seas of Athas before any sort of gargantuan terraforming project by the mind lords).
What you get as a result is the unenviable position of having to make a LOT of assumptions, and making decisions on how much realism vs fantasy you want in your game. I think 4e went the route of the silt sea actually being the “body” of a primordial? Troy Denning I think said something once about how a passage in the Amber Enchantress was meant to imply that the silt sea was a result of defiling magic’s effect on primordial water? City by the Silt Sea flat out says that the “bay” of silt that Giustenal is on the shore of could actually support water to the point that a powerful enough water cleric could actually “resurrect” the sunrise sea, at least in part. There are numerous instances of open water existing on the silt sea (vanishing lake being the most obvious). If you look at Tim Brown’s Dragon Kings project, one of the major themes that seems a holdover from his initial vision of Athas is that there are outside forces literally plundering the natural resources of the planet: an outside force siphoning off Athas’ natural resources would explain a lot, from the vanished seas to the almost nonsensical lack of metal and resources as a whole.
Personally, I think the silt sea is best as just the sunrise sea. I think there is a magical explanation for it, somehow linked to Borys (I think the Keltis explanation is bad, for multiple reasons). I think there must be other large bodies of water on Athas, just undiscovered for whatever reason, but that the majority of the former ocean floors are bare, as in the Kreen Empire.