If any of these spells/enchantments were to stop the inhabitants wouldn't be in a happy place. A prudent enchanter would have a backup with a trigger set to go off when water starts spilling into the covenant.
And if people need to make it a Ward, don't ward against water, ward against lakes. You don't want the lake getting in.
I looked a bit at this problem at one point. After some ruminations, I decided I'd prefer to build my covenant/whatever under the sea. The idea being warding against salt water, allowing fresh water (for eg drinking) to pass through unhindered. :-/
It does occur to me that you can use perdo to get rid of waste, and use a CrAq to create a spring inside the boundary if water cannot cross (other things can still be shipped in or out). Otherwise you have the amusing situation where you get a drink of water by taking a deep breath before stepping through the barrier to get a drink then stepping back through.
Yeah, I guess it would be SG decision whether lake water is ontologically distinct from water that is not from a lake. Considering that there are lake spirits, and spells to talk to lakes, it's not an unreasonable interpretation of Mythic physics, though nor would I expect consistent SG approval. Noteworthy though is that if lake water is ontologically distinct, it must turn any water it touches into lake water by definition, so your covenant wouldn't be able to be supplied by rain or ground water from the actual site, because the ground water is lake seepage and the rain water turns into lake water when it hits the lake.
So you'd probably need to lab-preserve an Arcane Connection to a totally different non-lake source of water somewhere else, and enchant something to summon water from there to the covenant.
Or just use vis to CrAq a spring inside the covenant that will not cross the border.