Ha, interesting, I read the same note...but contrary to you I apparently am capable of understanding simple geography. Since Far Cry 3 we all know what a cenote is (basically a deep and rather big hole in the ground, filled with water), and "in the north of" is also not all too hard to understand, so I headed to the north of Varshakot, to find this Cenote.
Eventually I got there and saw the underwater door but nothing else. The door cannot be opened, sadly.