As long as you come up for air every now and then, I see no harm in it. In fact, I've found that a dip in the pool not only feels great, but actually makes me feel like I've got a little extra energy.

Now, if you're talking about a hard core training session in the pool, that might be a different thing altogether. Still, you won't "undo" any training with that. You'll only further wear yourself out, and probably exhaust some other muscles that you didn't wear out on the bike.