I don't think this is a bug. Same thing for the Dead Sea Natural Wonder. They're treated as fresh water but not aqueduct-available.
If it's not a bug it's a change that wasn't pointed out. Crater Lake does count as Fresh Water, for settling purposes, but that distinction doesn't decide whether or not you can aqueduct to it, that would be the tile type (which is very weird with Natural Wonders.) It is a Lake Tile in fact, and that distinction of base tile type is what "should" and DID allow aqueducts to "attach" to it. Note: This can get confusing and honestly, Natural Wonders have always seemed sloppily put into the game, they have been tweaked but never overhauled, which should have happened when they added Gathering Storm, where storms/disasters improved/removed yields from tiles, and they added in a new Tile Type Volcano, but it's still a base Mountain tile. Tile type is kind of like a Feature (ex: Forests.)
Wonders as examples:
Firstly, Crater Lake does provide adjacent Fresh Water, but the Tile Type is a Lake Tile, (but also itself, a Natural Wonder.) (Separately, this wonder is found on Flat Plains/Tundra, for it's Base Tile, without the base yields from Flat Plains/Tundra or as a Lake.) It is effected by Huey Teocalli (Lake Tile yields), but like other lake tiles, effected by the Lighthouse/Shipyard/Seaport yields as they effect Coast & Lake tiles. In addition to being Suzerain of Auckland the production bonus yield.
Secondly, the Dead Sea, like the Lake Retba natural wonder, does provide Fresh Water in the versions of the game prior to Gathering Storm (making it's Tile Type Lake.) BUT, when GS was release this was changed, so that the Dead Sea does not provide Fresh Water (its' Tile Type was changed from Lake to Coast, thus giving it only a +1 House modifier.) This would mean since GS was released, those that have bought GS had this Tile Type changed for this Natural Wonder, and of course, would no longer be able to aqueduct to it. It's Base Tile is either Grassland/Desert, but being a Coast Tile is still affected by the Lighthouse/Shipyard/Seaport, as well as, being Suzerain of Auckland. And because it is a Coast Tile, it doesn't get effected by Huey Teocalli, but is effected by Mausoleum at Halicarnassus for the same reason. (This is a weird one, because Ocean and Coast are Base Tiles and Tile Types, from my understanding. And the only water features (that aren't Natural Wonders,) that can go on land are Lakes and Oasis', but this Natural Wonder, is either Grassland/Desert AND Coast for Base Tile, and like I said a Coast Tile is also, itself a Tile Type, which isn't exactly a Feature but close, because a Reef is a Feature and that only spawns in, in Coastal tiles. I know, this hurts the head.)
Fountain of Youth, just to be clear is neither Coast nor Lake, it's kind of like an Oasis Feature, but instead of being just on Flat Desert it can be on a Flat Grassland/Plains/Desert. Just like an Oasis, it does provide Fresh Water and you just walk over it with no Embarking, thus why I compared it to the Oasis, except its' Feature is that it is the Natural Wonder and it still won't (like all Natural Wonders) get any base tile yields that aren't its' own. (Note: I have yet to run into this Natural Wonder spawning in a game as a Flat Desert Tile, but it should be possible as it is labeled. The reason i mention this is, that by my understand, if it were to spawn in like that on a desert tile next to or in the desert, Nazca's, Nazca Lines could and should buff the tile's yields. As well as, any Natural Wonder if the locations line up for the Natural Wonder and free adjacent Flat Desert tiles.
Ik-Kil, you may be wondering is actually a Rainforest Tile Type, of which its' Base Tile is either Grassland/Plain. Obviously, the this Tile Type cannot be aqueduct to. It does 'provide Fresh Water' though, and it's other bonus. This is not improved by Chichen Itza, because it is an impassible tile and can never be worked, and they never would let that, as workable Rainforest Tiles are always Plains, and this Natural Wonder could be on Grassland.
Lake Retba, like we talked about with the Dead Sea had the same change from Tile Type Lake to Coast in GS, so if you have and use GS you it will not provide Fresh Water, you may not aqueduct to it, and will provide just a +1 Housing modifier. It's Base Tile will either be Flat Grassland/Plains, (but of course as we head achingly discussed, also Coast.) And thus, is affected by the same yield modifiers as the Dead Sea; the Lighthouse/Shipyard/Seaport builds, being Suzerain of Auckland, not Huey Teocalli but the Mausoleum at Halicarnassus.
Giant's Causeway, has 1 Base Tile as either Flat Grassland/Plains and there other as Coast, but it is an impassible tile and not a Mountain Base Tile, which never gain yields or be able to be worked.
Pamukkale, has Base Tiles as Flat Grassland/Plains/Desert, but again, is an impassible tile and not a Mountain Base Tile, which never gain yields or be able to be worked. Though it does provide Fresh Water, it may not be used for an aqueduct as it it neither a Lake/Volcano Tile Type nor a Mountain Base Tile.
Galapagos Islands, are Coast Tiles but impassible, so again, not a Mountain Base Tile, while never get yields itself.
Great Barrier Reef, is a Coastal tile through and through, Base and Type, so quickly, yes to the Lighthouse, Shipyard, & Seaport buildings, being Suzerain of Auckland, and the Mausoleum at Halicarnassus. BONUS: In the new February 2021 Free Update, this Tile Type should change to being a Coastal Reef, no added yields just like an Natural Wonder, they do not get yields from neither their Base Terrain Tile nor their Type Type/Feature, but that means Campuses get a Major (+2) adjacency modifier from it now and "might" like a Reef, gain a Defensive Modifier of +3 and if the city has an Aquarium, an extra +1 Science Yield, or it will be like the marshy Pantanal or Ubsunur Hollow and not work that way. (But we shall see.)
Cliffs of Dover, only thing water tile related to mention is that they always have cliff borders on the sides adjacent to Coastal tiles (no idea about Lakes, never seen that happen before.)
Lysefjord, has Base Tiles being Flat Plains/Tundra & impassible, thus cannot ever have yields or be aqueducted to since not a Mountain Tile Base.
Bermuda Triangle, not much to say Ocean Tile Base, rarely in range of cities to work, which is a bummer.
Ha Long Bay, is a Coastal tile through and through, same as the Great Barrier Reef, minus that the GBR is changing into also being a Tile Type Coastal Reef.
Piopiotahi, has Base Tiles being Flat Grassland/Plains & impassible, thus cannot ever have yields or be aqueducted to since not a Mountain Tile Base.
-That should be all the Coastal, Lake, Ocean, or "Fresh Water Providing" Natural Wonder. As you see, Crater Lake, being a Lake Tile Type(Feature) should be able to have an Aqueduct connected to it. As, for an Aqueduct, the need is a River, Mountain Base Tile, Lake Tile Type, or Oasis Feature. If the Natural Wonder has this in their code, it 'should', but sometimes devs miss things, should be noted in the in-game information. If it says, "acts like", that's what they mean, "acts" doesn't mean it does everything just like the reference.
-To make it obvious, just because it is in the name or the game text says it "acts like" does not mean it works as if it is that Base Terrain or Tile Type, ex: Lake wonders aren't all really Lake Tile Types, Pantanal/Ubsunur Hollow may says 'acts like' and even has a Marsh Tile Type with the -2 Defensive modifier that marsh tiles have, but it's NOT a "true marsh" in the sense of it could be found on a Plains/Grassland for Pantanal or Tundra/Grassland for Ubsunur Hollow, when true marsh tiles only have their Feature on Grassland tiles, plus they both give off +2 Appeal per each tile, unlike with true marsh tiles that actual give off a -1 Appeal. Plus you cannot get yields as a Marsh from neither the Pantheon, the Lady of the Reeds & Marsh nor the +1 Science from the Zoo building.
(Personally, I think they should count towards the Pantheon and Zoo building. For as besides the Appeal thing (which it's a Natural Wonder, of course it would be positive, but it's still just +2 and not one the the +4 Natural Wonders,) they pretty act like true Marsh Tiles, except you of course can't harvest/remove the 'feature'. IMO, those 2 Natural Wonders, could use the extra +2 production from the Pantheon and the late-mid-game +1 Science from the Zoos. Hardly, OP. Especially compared to all the bonuses yields you can get on other passable natural wonders' Ha Long Bay, Great Barrier Reef (hope the Aquarium Yield & Reef Def Mod are added with the Feb 2021 change), Lake Retba, Dead Sea, & Crater Lake.
-Also, now which version of the game you are playing, though I assume 99% have up to at least, Gathering Storm these days, as it does fundamentally change Lake Retba and Dead Sea, as well as, the Frontier Pass, adds 2 new Natural Wonders.
-As far as yields, the Base Yields of a Natural Wonder's tile are the Natural Wonder's yields. They get none of the starting yields from the Base Terrain Tile, the Tile Type, or any represented Feature. But the Tile Types and represented Features, maybe be modified accordingly through out the game, IF they are passable natural wonders. Though it is notable, that to my belief, the natural events; Blizzards, Dust Storms, Volcanoes, and Hurricanes will never add yields to Natural Wonder tiles themselves, but neither will they loss yields to Droughts nor ever be flooded due to climate change.
-I did mentioned Nazca Lines, because their yields are provide by being built adjacent (which is quiet unique,) but you can never improve or put districts on top of Natural Wonders, not matter their Base Terrain Tile.
-Last thing, this is about all the mountain looking natural wonders. They almost all say "act-like mountain", but they are almost all Not Mountain Tiles. You cannot aqueduct to them nor do they count as a mountain for district adjacency purposes. I figured that out a long time ago when I took the Pantheon that gives Holy Sites +1 faith from adjacent desert tiles, and they already got +1 from mountains, and a tile could have both giving you, if all tiles around it were desert and you had 3 mountains as those tiles, a +9 Holy Site, even before district adjacency. But it you tried that with Natural Wonders, you would get just the normal +2, not +3 because it's desert or +4 for being a desert mountain natural wonder. The natural wonder, kind of trumps the others in terms of Adjacency counting. Though to note, Non Madol, will give you the +2 culture to any district next to coastal natural wonder, including Lake Retba and Dead Sea, as well as, the extra +1 culture from Rapa Nui's Moai next to these for counting as next to Coast. Other note: Indonesia will get to stack their Coast/Lake District Minor adjacency with these Natural Wonders too, as well as, Gitarja's City Center Faith, if settled next to. Example: If you place a Holy Site as Indonesia, adj to both Lake Retba tiles, you get +2 from both tiles, plus .5 from each for being Coast and the Holy Site is obviously a district making it a +5 faith Holy Site. (There is only a 20% I'm wrong with this, I remember doing this, but honestly, the way the Marsh and Mountain ACTING Natural Wonders work, it shouldn't. LIKE I SAID, NATURAL WONDERS = MESS!) GG