I am now on the island Carbonek and I have just gone through inside a river to get to a cave so I can save the Queen Rhea. So I believe this is the game you were talking about: Atlantis The Lost Tales (Atlantis 1).
It is possible you also go through water in the other Atlantis games, but as soon as I read your first post I only thought of the first one. I think the constellations are behind the throne when you are trying to escape the palace on Atlantis.
I bought it from Gog and it works without problems on Windows 8. It is so weird to play it in English, I have played it dozens of times in French. My screen is large and it is pixelated, the solution is to move away from the screen. I play from the sofa and it is still as beautiful as I remember. I love the threat of storm with thunder on the island. I think it rains later on too.
There was a point when I was younger when I would have given anything to live on Atlantis and the island Carbonek of this game. And I certainly did, albeit only virtually.