That's a lot of time to drink some water!
I think that as long as you don't use it as an excuse to just take a break (specially if you're a marathoner) or don't let you heart rate fall too much, I think it's fine.
The two main goals of the long run (besides the aerobic development) is to get used to run with depleted glycogen stores and to exhaust the slow twitch fibers in order to force the recruitment of fast twitch muscle fibers and I don't think that a quick pause will affect any of these things.
Before some guys come roast me about the fast twitch stuff, Daniels says it if not in one of the editions of his Running Formula in one of his lectures on YouTube.