I can confirm that I also get this all the time when in the "cave" template style dungeons (especially ones with water in them). However, there is one thing the OP didnt mention (not sure if he has this issue as well) but when I hear the water sounds I also sometimes see a visible water line apear on my screen. It's so quick that it just looks like some blue stuff flickering on the screen. I have no mods. I play completely vanilla.
Also, after having played oblivion and skyrim for so long I can tell by the sound its the one you hear when you submerge or emerge through a water line. I'm almost certain that this is the sound. It almost seems like I'm clipping through the floor at times and hitting water underneath the map. I've seen stuff similar to this in other games. Just my hunch.