This is something I've actually been thinking about as well, especially since CS:GO doesn't have any maps with swimmable water at all anymore.
In my opinion, water serves a good purpose in TF2 since fighting underwater is actually possible with TF2's style of combat, but since it's inherently more awkward to fight in than on land, it can make for some interesting flank routes (like on cp_well or cp_freight for example) that aren't used very often due to that fact.
It also extinguishes fire, jarate and mad milk which can be very helpful if a pool of water is placed tactically in a highly contested area, especially if you want to reduce the effectiveness of pyros in that area.
But of course, competitive players are very picky when it comes to map elements that change their playstyle, so I'm not sure if the competitive community would agree with me on this topic.