Sorry if this is a known issue, I tried search, but couldn't find anything.
Almost always when I go to a beach, I won't see any water or it is there for a short moment (< 1 minute) and then vanishes. This seems to be not only a display problem, but unless the sea west/north-west of NT is very shallow seems to bug the "hold your breath" timer as well.
A while ago I was looking for Sadie's Serene Spot and after not finding it checked the wiki for coordinates. At that time the wiki had the wrong ones, namely 45.037, 15.398. I went there, but of course couldn't find anything, being far from the coast. Even after alt-tabbing for about 2 minutes to confirm the coordinates from another source I was still alive and had no timer either.
Water in ponds and rivers seems not to be affected, at least I have never seen the NT pond empty.