Water in Bloodborne: Oceans Aren't The Way
If you look out from Lumenwood Garden on the way to the Fishing Hamlet, on the right you'll see floating islands with "cities" on them. On the left, you'll see a few cities on islands within what seems to be an ocean, overlooked by a shining sun. You can still see the light of the sun as you prepare to exit into the Fishing Hamlet, and as you cross the threshold, it momentarily blinds you, but then... you see only water. The radiant sun is replaced by rainy skies. The cities to your right and left are still there-- only now underwater.
The change of perspective between Lumenwood Garden and the Fishing Hamlet raises the question: how can a city be in open air and underwater at the same time? The snail that mysteriously falls from the sky near the Whirligig Saw in the Hunter's Nightmare suggests that the place is under the Fishing Hamlet, ie, that it's underwater. But that snail was falling, not sinking, and you certainly don't seem to need scuba gear. Perhaps our understanding of water needs some refining...
What is Water?
Great volumes of water serve as a bulwark guarding sleep, and an augur of the eldritch Truth.
It seems to me that the traditional interpretation of this phrase has been that it refers to oceans or lakes. But this interpretation is insufficient, because it explains too little. For the most-repeated phrase in all item descriptions, are we really to interact with it only once and weakly at that, when fighting a braindead spider? I think we can do better. Let's attack the problem from another angle.
"The Sky and the Cosmos are One"
For the majority of us who grew up in the Western cultural and literary tradition, the above line seems somewhat redundant. We've generally considered that the gods live on some really big mountain, in the clouds, or just somewhere up there, so it means very little to affirm that the sky and the heavens (or cosmos) are the same.
But there's one thing somewhat unique about the sky in Bloodborne: it's always cloudy (except in Forbidden Woods, where it's foggy instead), and the clouds are generally quite dense. Even if you take the naive ending and wake to the morning sun, there are still clouds. This unnatural universality allows us to better understand the role of clouds: physically, clouds in Bloodborne are always there to separate us from the sky-- or, to the Choir, they are always there to push us away from the cosmos and all the secrets held within. This corresponds to the role that the Lake runes assign to bodies of water. And scientifically speaking, clouds are quite literally "great volumes of water".
Remember the floating islands to the right of Lumenwood Garden, and the waterbound islands to the left? It's a weird asymmetry. But as soon as you consider that clouds are just water, right and left are basically the same, and the otherwise inexplicable asymmetry is resolved. Moonside Lake's "sky" also seems to contain cloudlike structures, notably towards the horizon. If we consider that clouds are the "same thing" as oceans, the contradiction of an underwater sky no longer exists.
Now the Lake runes become much more applicable, and the paucity of relevant oceans in the game is no longer an issue to the supposed importance of water, since we have plenty of bulwarky clouds. (Otherwise, Moonside Lake is the only example of an ocean that blocks access to something eldritch.) In the most pertinent example, The Hunter's Nightmare, Fishing Hamlet, Nightmare Frontier, and Nightmare of Mensis are stacked on top of each other, the eldritch truths of the next layer up bulwarked away only by clouds.
If you look out at the moon from the Wet Nurse's Lunarium, you'll notice that it's below the clouds, but also above a different layer of clouds. This is absurd on a scientific level. But with our metaphorical reading, it makes sense to consider that this place is some kind of cosmic eldritch truth beyond which other truths exist, blocked off by great volumes of water in the form of clouds. Thus, the scientific absurdity can be read to reinforce the thematic nature of the level.
We look down from Hamlet and see a city underwater, whereas we look up from the Nightmare and see billowing clouds. This initially confounded us, but now we've established that the game's distinction between clouds and oceans is only a facade, that they're the same thing from different perspectives. It's not clear what rules govern this difference in perspective, but it may be related to one of the core themes of the game: the incomprehensibility of the truth.
A special weapon used by the Choir, high-ranking members of the Healing Church. Sprays a cloud of sacred mist, created by using blood-imbued Quicksilver Bullets as a special medium.
Arias are heard whenever sacred mist is seen, proving that the mist is a heavenly blessing. "Oh, fair maiden, why is it that you weep?"
Why would mist, of all things, be "sacred" or "a heavenly blessing"? The only other things described as sacred in item descriptions are the Yharnam Stone (for obvious reasons) and Healing Church rituals (in the Loch Shield description, again for obvious reasons), and the only other blessing described is "making contact with eldritch wisdom" (Madman's Knowledge). Why are Quicksilver Bullets and Blood Vials mundane, but heavenly when turned into mist?
Now we know: it's because mist, with its construction so similar to clouds, is too a marker of the divide between us and the eldtrich.
The impact of this perspective is, as just demonstrated, that we can now meaningfully analyze the usage of the other forms of water in Bloodborne. The game has many different skies and many different types of clouds, and I hope that I've been able to lay some groundwork for further investigation of their implications on lore and literary meaning. If I knew anything about cloud types, I would try, but I think I'll leave the nephology to those who are capable :P