Nadal powered 39 winners past Marterer, who pushed the Spaniard as hard as he could without ever threatening an upset. She broke straight back, winning on her first match point when Mertens double-faulted. I am in quarter-finals.
The Spaniard will play 11th seed Diego Schwartzman, 25, in the last eight.
The German, who has previously stated his desire to be the best in the men's game before Nadal and Federer - now ranked number one and two in the world respectively - retire, once again stated his intention to do so during the French Open that is underway in Paris.
The win means Nadal will now face Argentina's Diego Schwartzman, who earlier staged a thrilling comeback from two sets down to stun sixth seed Kevin Anderson and reach the last eight.
The top seed had few problems in serving out the set and he made a flying start to the second with another break to love as Marterer got a first-hand look at why the champion has been dubbed the King of Clay.
The first went begging with a forehand long of his own, but Marterer's fight was finally over when he could not land a backhand, prompting Nadal to race to the net and congratulate the German on a fine effort.
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But as in the first set, Nadal's riposte was swift, chasing down a drop-shot to set up a break-back opportunity, converted when Marterer thumped a forehand long.
The big South African stormed to a two sets lead and served for the match in both the third and fourth sets.
"Did you read David and Goliath?" I honestly didn't think I played badly this morning.
Marterer, enjoying his best run on just his third appearance in the main draw of a major, performed with admirable composure and maturity that belied his 22 years and did force another break midway through the third set but ultimately could do little to halt the Nadal juggernaut.
The German youngster quickly discovered just what it feels like to be on the receiving end of a pummelling by the veteran though, as Nadal swept to a 6-3, 6-2, 7-6 (4) victory to reach the quarter-finals in Paris for a 12th time.
Nadal won the French and U.S. Open in 2017, while Federer won the Australian Open and Wimbledon.