to flow over something, or to bring something up so that it rides on the surface of the water
All three appearances of this verb have water in view, and all three are about what ends up on top.
- The sea is made to run over Pharaoh's chariots as they chase Israel (Deuteronomy 11:4).
- Water closes over the head of a man who believes he is finished (Lamentations 3:54).
- A borrowed iron axe head, sunk in the Jordan, is brought back up to ride on the surface (2 Kings 6:6).
What holds these together is the line where water meets whatever it covers. In the first two the water crosses that line and stands above its victim, so the word means engulfing, drowning, being overwhelmed. In the third the movement runs the other way: something heavy comes up through the water and stays on top of it. The word names the result rather than the direction, which is why English needs two different pictures to carry it.
The reversal in the Elisha story is worth noticing. The verb used when God drowns an army at the sea is the same one used when a prophet brings a poor student's borrowed tool back up out of the riverbed. Hebrew has a common verb for water that sweeps things away (שָׁטַף), used dozens of times; this one is rare enough that each of its three uses stands out on its own.
A noun spelled exactly the same way (צוּף) means a honeycomb, or the honey that drips from one. Older lexicons explained that noun as the thing honey "flows" out of and so traced it back to this verb, but the connection is an old suggestion rather than a settled fact, and none of these three verses has anything to do with honey.