If I'm not mistaken, you can have water at different heights so long as it's all within the same visleaf. Once the player enters another leaf you'll notice the water changes. You can see all the leaves with the console command mat_leafvis 3, btw. I'm betting you'll see a red line right through the middle of that screen shot if mat_leafvis was turned on.
An easy fix is to use what they call "cheap" water instead, which is the one that of course doesn't look as nice. You can have "expensive" water brushes with multiple heights, but they have to be within the same visleaf. And I believe visleaves have a max size of 1024 units (volume), so you have to fit all the water brushes into that, and everything within that volume would have to be a func_detail so you don't get extra BSP splits. So, kinda complicated for the nice "expensive" water brushes, but I believe it's do-able if your water doesn't cover a volume larger than a 1024 unit cube (has to be aligned on a 1024 unit boundary too).
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