You'll need to determine where the leak is occurring. This can be quite difficult to find so I suggest if you don't see any obvious issues, taking this to a shop that specializes in Mercedes.
Here are some in your area: http://repairpal.com/directory?address=32963&car_brand_names=Mercedes-Benz
I have disassembled major body components and see nothing that indicates where leek is coming form. I'm looking for assistance to do it myself. After removing plastic firewall grill mounted between windshield and hood I have discovered a rubber nipple on left and right side. If this nipple is not properly sealed, could this cause water to flood floorboards?
The only way I've ever found water leaks is to put a garden hose on the car and let water pour onto the area where you think it is leaking. Get inside the car, and try to find where the water is coming from. You may need to remove many parts (panels, covers, carpeting etc.) to see where the leak is occurring. Focus on door, window and sunroof seals - sunroof drains - front cowl drains.
I think the parts you're talking about are the cowl drains, make sure those are clear and sealed OK, they will definitely cause this issue.
i have a 1998 ml 320 with 2 problems. the 1st being that after a few weeks of on and off rain my car somehow accumulated a lot of water and it was slosh around whenever i would turn, or stop. turns out there is a drain under the rear passenger door underneath the car which was plugged and about a gallon of water drained out. problem 2, after it rains i get water leaking onto the passenger floor. i have discovered that it is coming in from underneath the dashboard. there is a panel where the 12 volt plug is. i don't not know from where this water is entering however. could be windshield seal or some thing else. this problem really sucks and i neeeeeeeeed to get it fixed because it is driving me crazy.
It is the intake area under the wiper blades; the drain is on the passenger side. (check out this photo http://www.benzworld.org/forums/attachments/w220-s-class/192528d1219845433t-2000-430-water-car-3.jpg). I stuck a plastic rod in the hole to unclog it. I found that leaves and other debris were simply blocking the valve opening
I have a 2000 ML320 and I found the drain tubes that run from the front of the sunroof pop off at the fender where they go through. You can get to them but it is a pain. In the passenger side it is about 9in. above the fuse panel in the kick panel. Same position on drivers side is "easier" to reach. I extended the hose a little with hose barb and extra hose and reconnected it to the original hook up.