In SMP, when riding a boat through shallow and narrow water (especially in swampland biomes), there are certain spots where the boat collides with an invisible block. This block (or whatever it might be) cannot be seen or interacted with but with the boat. So when swimming through them without a boat (usually after crashing and destroying it), there seems to be nothing there.
Note that even at very low velocity, and after entering the boat just a few blocks away, the boat still won't pass. Also, the position of this invisible walls stay the same after reconnecting.
This might be connected with the bug that makes other players and their boat/minecart invisible, as the remains of a boat that crashed into such a block sometimes (not always!) appear several blocks aside the place of the crash.
This bug was observed on one map so far (Seed: 4), in SMP.