Any screenshots?, or a youtube video of the problem?
I would make a full compile on at least the area with the water, using cordon bounds. I usually do a lot of full compiles before the map is done, because the errors you find on the way are faster to fix than waiting for a full final compile and working on it afterwards.
Water problems are usually because of leaks. But just in case, make another water surface nearby and see if it also has problems.