Sounds a little scary. Do you recall where, front or back, driver's or passenger side of the engine the noise was coming from? Did it seem to get louder and clunkier as the engine slowed, seeming to be tied to engine speed?
These things can be hard to understand when you are there, in person, and from the other side of an internet connection it is even more difficult.
I agree with jbaj007 that it sounds like an accessory drive from your description, than an internal engine issue. Did you check the single, serpentine drive belt and the pulleys it is wound around? If one has come loose or the bearings are shot, it might make a clunking noise.
Good luck, Jim
1986 Euro 190E 2.3-16 (291,000 miles),
1998 E300D TurboDiesel, 231,000 miles -purchased with 45,000,
1988 300E 5-speed 252,000 miles,
1983 240D 4-speed, purchased w/136,000, now with 222,000 miles.
2009 ML320CDI Bluetec, 89,000 miles
1971 220D (250,000 miles plus, sold to father-in-law),
1975 240D (245,000 miles - died of body rot),
1991 350SD (176,560 miles, weakest Benz I have owned),
1999 C230 Sport (45,400 miles),
1982 240D (321,000 miles, put to sleep)