At the 2008 Short Course World Championships, Nathan won two gold and one silver medals. In the 4x100-meter free style relay, he joined with Ryan Lochte, Bryan Lundquist and Doug Van Wie, and together they won gold in a world record time of 3:08.44. In the 100-meter freestyle, he won gold in a time of 46.67. In the 4x100-meter medley relay, he joined with Ryan Lochte, Randall Bal and Mark Gangloff, and together they won silver behind Russia.
At the 2008 United States Olympic Trials, he placed fourth in the 100-meter freestyle, which qualified him to swim for the 4x100-meter freestyle at the Olympics. He also placed sixth for the 50 meter freestyle.
At the 2008 Summer Olympics in Beijing, he swam the first leg in the preliminary heats of the 4x100-meter freestyle relay with a time of 48.82. Cullen Jones, Benjamin Wildman-Tobriner and Matt Grevers finished it off with a final time of 3:12.23, which had set a world record. This record was broken one day after when Michael Phelps, Garrett Weber-Gale, Cullen Jones and Jason Lezak swam a time of 3:08.24, beating France and Australia in the final. Nathan still earned a gold medal by swimming in the heats, even though he did not swim in the final.
Nathan took the 2008 year off college to train under coach Mike Bottom in the Florida Keys as part of The Race Club swimming training program World Team prior to the 2008 Summer Olympics.
At the 2009 National Championships, Nathan placed first in both 50-meter and 100-meter freestyle events, which qualified him to swim at the 2009 World Aquatics Championships in Rome.
At the 2009 World Aquatics Championship, he won gold in both the 4x100-meter freestyle relay and the 4x100 -meter medley relay. During the 4x100-meter freestyle relay, the United States was behind the Russian team by a few seconds after Michael Phelps, Ryan Lochte and Matt Grevers finished their legs, but Nathan swam in 46.79 to go beyond Danila Izotov for first place. The final time was 3:09.21, and it marked as a championship record. In the 4x100-meter medley relay, Nathan joined Matt Grevers, Mark Gangloff and Tyler McGill, and together they earned a gold medal when the U.S. placed first in the final. Nathan also placed sixth in the 50 meter freestyle and tenth in the 100 meter freestyle.
At the 2010 National Championships, Nathan was qualified to compete at the 2010 Pan Pacific Swimming Championships by winning the 50-meter and 100-meter freestyle titles. His win in the 100-meter style also guaranteed him a spot on the 4x100-meter freestyle and 4x100-meter medley relay teams.
At the 2010 Pan Pacific Swimming Championships, Nathan won a total of four gold medals, which is the best performance of his career. In the 100-meter freestyle, he won the gold in 48.15, beating Canadian Brent Hayden and world-record holder Cesar Cielo. He then joined Michael Phelps, Ryan Lochte and Jason Lezak in the 4x100-meter freestyle relay. He recorded a time of 47.51, and the team won the gold in a time of 3:11.74. Nathan surprised Cesar Cielo in the 50-meter freestyle final by winning first in a time of 21.55 seconds; Cielo finished in 21.57 seconds. He later competed in the 4x100-meter medley with Aaron Peirsol, Mark Gangloff and Michael Phelps. He recorded a time of 47.54 in freestyle, which was the fastest in the field, and the team won the gold in a time of 3:32.48.
At the 2011 World Aquatics Championships, Nathan won a bronze medal in the 4x100-meter freestyle with Micahel Phelps, Garrett Weber-Gale and Jason Lezak. He swam a record time of 47.40. He placed sixth with a time of 48.23 in the final of the 100-meter freestyle, which was off from his semifinal time of 48.05. In the 50-meter freestyle, he placed fourth in a time of 21.93 seconds, just one one-hundredth (0.01) of a second behind Alain Bernard. In the 4x100-meter medley relay, Nathan joined with Mark Gangloff, Michael Phelps and Nick Thoman to win gold in a time of 3:32.06. Nathan had a time of 47.64.
At the 2011 National Championships, Nathan moved to the fourth spot in the world behind Cesar Cielo (21.52), Bruno Fratus (21.76) and Frederick Bousquet (21.78) when he came in the time of 21.84 seconds in the 50-meter freestyle. He chose to sit out of the 100-meter freestyle to prepare for the 2012 Summer Olympics.
At the 2012 U.S. Olympic Trials in Omaha, Nebraska, Nathan made the U.S. Olympic team for the second time by finishing first in the 100-meter freestyle. In the final of the 100-meter freestyle, he finished at 48.10 seconds to finish ahead of Cullen Jones, who finished at 48.46. He also placed third for the 50-meter freestyle with a time of 21.68, therefore missing a spot in that event.
At the 2012 Summer Olympics in London, Nathan won a total of two gold and one silver medals. His first medal, a silver, was the 4x100-meter freestyle relay with Michael Phelps, Cullen Jones and Ryan Lochte. He recorded a split of 47.89 seconds, and the team finished with a final time of 3:10.38. Nathan’s split was the only one in the race that was under 48 seconds, and it was his first time doing so.
Nathan’s first gold medal was in the 100-meter freestyle final on the fifth day of competition. He defeated James Magnussen of Australia by one one-hundredth (0.01) of a second. He became the first American male to win the event since Matt Biondi did in 1988. He had set a new personal record of 47.52 in the race. He was second with a time of 47.97, which was the second time he ever broke 48 seconds in the event.
His second gold medal was winning in the 4x100-meter medley relay. He swam the freestyle leg with Matt Grevers swimming backstroke, Brendan Hansen swimming breaststroke and Michael Phelps swimming butterfly. The team recorded a time of 3:29.35 with the Japanese taking the silver and Australians taking the bronze.
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