In many games where the player can go underwater, it seems like when you look where the top half of the screen is in the air, and the bottom half the screen is in the water, it's almost like the water doesn't exist and the player is... flying slowly with water sounds?

Is there a logical way to solve this? An algorithm? Doesn't seem like any solution has come up yet since many games still have this. I don't want to make the same mistake.