footloose,
About 5 miles south of Duck key, on the ocean side is Boot Key Harbor. Marathon Boat yard is located in this area as well. This is just on the south/east side of US#1 and just before the 7 mile bridge. There are anchorages that are well protected inside this area. Otherwise, depending on the weather, you could anchor on the gulf side just north/west of where the former Faro Blanco is located. Water depth is 7' plus, with pretty good holding. Also just north of the cut that goes from the gulf to the ocean in mid Marathon is another semi protected area with 7' plus depth and good holding. Have fun!