Shertex, I also have a 95 E300D that was getting some water in the footwell. Water was ingressing below the rubber seal at the base of the windshield, specifically in the area of the wiper, and getting into the cabin air filters. The wet filters were also causing the windows to fog whenever it rained.

In my case, the windshield had been replaced by the PO with a non-MB part which did not incorporate the flange at the bottom of the windshield to which the rubber seal attaches. The installers had used windshield sealant to stick the rubber seal to the windshield but did a very poor job of it, leaving gaps in the sealant for water to flow through.

My solution was to purchase 3M Window Weld urethane sealant (Autozone, $25 or so) and run a continuous bead below the upper edge of the rubber seal to adhere it to the windshield. Worked great, no more leaks. It's reversible as well, I've had to pull it loose once to access the blower motor and the urethane separates cleanly from the seal with a little care.

Hope yours is this simple!