These great waters are supposed to be a lake, or some great pool in Gibeon, the very same that is mentioned 2 Samuel 2:13, where Joab and the servants of David met, the one keeping on one side of the pool, the other on the other side.
Related Commentaries of Jeremiah 41:12
Jeremiah 41:12
12 Then they took all the men, and went to fight with Ishmael the son of Nethaniah, and found him by the great waters that are in Gibeon.