It's the same for Planet Coaster. Frontier's game and software.... will only let you place the water height where IT wants to. Valid, valid... Obstruct.
But at least they've improved the height we can now place it, compared to Planet Coaster, it's a tad bit higher where we can put it.
One tip is to make your water beds on the foundation of the map. If you try to add it to raised land, what happens in Planet Coaster is you'll have to place the water height next to like cliffs. Planet Zoo the water height... grrr... as I'll put, is higher. But it would be awesomeness if they updated the software in the game to allow us to place the water level at the top, rather than be fussy.