It's all in the spin, and to a lesser extent Nadal's speed and mobility on clay. A high RPM top spin shot will kick forward and bounce high on clay to a greater extent than on a hard court, and it's extremely hard to deal with.

I have hit with some pro tour players on clay, once even a former world #1 player, and it's near impossible to play offensively against their spin unless you want to take every ball on the rise.

Also Nadal's flat serve is probably the weakest of the 3 greats, but the importance of a good flat serve is somewhat de-emphasized on clay.