The name Mark Twain came about as it was an old Nautical term, as stated above. They would mark depth on the Mississippi River by dropping a demarkated rope in the water. Now, a Mark Twain is two fathoms, or twelve feet. Samuel Clemens was a boat skipper, and he chose this name, because at Mark Twain, it was safe to sail along.

The old nautical depth measuring system works like this:
One would drop a rope into the water, and see by where the water came up to as how deep it is. The marks on the rope were at 2, 3, 5, 7, 10, 13, 15, 17, 20, 25, 30, 35, and 40 fathoms (as implied above, a fathom is six feet). If it came up to a mark, the leadsman (the person in charge of measuring depth would yell "by the Mark Twain" (for two, or whatever it happened to be). Ever hear of the term "deep six"? Well it also came from here. A "deep" is something that didn't come up to a mark. A leadman could yell "by the deep six!" Meaning that it did not come up to a visible mark, but was 36 feet deep.

Modern depth measurements are done by sonar.