The vacuam lines do run through the rear floorboard, but I can't imagine that causing the problem you described.
BTW I dealt with back floorboard water after rainstorms for years. Finally thanks to this forum, I cleaned out the drain ports under the hoodhinges and just inboard from there with a piece of baling wire (for city people, a coathanger would probably suffice) and have yet to have reoccurrence of the problem.
'84 Euro 240D, 523K miles
'88 300E 5 Speed
'81 300D Daughter's Car
Over 800,000 miles in