Sometimes the entrance can be partly or completely obscured by a wall. Check the auto map, to see if you can see some blue sticking out somewhere. Running around methodically searching with the mouse can also help, though it sounds like you tried that already.
Occasionally the entrance can be a pile of rocks, rather than the usual fountain thingy.
Check the automap for locations you can not get to. Rarely part of a level can be separated from the rest, which could contain the entrance to the third level.
