Another explanation, because there is always somebody who doesn't get the word here is Owen a couple of pages later:
"God spared not his only Son, but gave him up to death for us all; that he made him to be sin for us; that he put all the sins of all the elect into that cup which he was to drink of; that the wrath and flood which they feared did fall upon Jesus Christ (though now as the ark, he be above it, so that if they could get into him they should be safe). The storm hath been his and the safety shall be theirs. As all the waters which would have fallen upon them that were in the ark fell upon the ark, they being dry and safe, so all the wrath that should have fallen upon them fell on Christ; which alone causeth their souls to dwell in safety."