Magnussen earned a silver medal, with Eamon Sullivan, Kyle Richardson, and Cameron Prosser in a time of 3:14.30, finishing behind the United States.

In the 4×100-metre freestyle relay, Magnussen won a gold medal with Kyle Richardson, Eamon Sullivan, and Tommaso D'Orsogna in a time of 3:13.92.

At year's end, Magnussen competed at the 2010 FINA World Swimming Championships (25 m) in Dubai, and was part of the Australian team that finished 5th in the 4×100-metre freestyle relay.

"[10] On the final night of competition, Magnussen won a silver medal in the 4x100-metre medley relay with, Hayden Stoeckel, Brenton Rickard, and Geoff Huegill in a time of 3:32.26.

[14] After topping the heats (22.19) and semifinals (21.87) in the 50-metre freestyle, Magnussen won the final in a time of 21.52, the fastest any Australian has ever been in textile swimwear in that event.

Issues pertaining to Magnussen's behaviour before and during the 2012 London Summer Olympics became apparent, due to reports that his Australian Swim Team teammates ultimately cheered upon his defeat in the 100-metre freestyle final.

[18] Magnussen was accused of having a "big head" during the games, with claims that "he did not feel the need to attend team meetings and that he did not want to sit poolside to watch other Australian swimmers compete".

[19] There were also some complaints about Magnussen and his 100 metre relay teammates, dubbed the Weapons of Mass Destruction,[20] who were accused of harassing other Australian swimmers who in return described the quartet as "out of control".

[20] In his first event at the 2013 World Aquatics Championships in Barcelona, Magnussen combined with Cameron McEvoy, Tommaso D'Orsogna, and James Roberts in the 4x100-metre freestyle relay, with the team finishing fourth place, repeating their result from the 2012 Olympics.

Swimming the lead-off, Magnussen recorded a split of 48.00, finishing behind American Nathan Adrian for the second-best opening leg.

In January, Magnussen opened the season in very sharp form, clocking 47.59 at the Perth Aquatic Super Series, followed by a 21.88 in the 50 m freestyle.

The Australian team swept the medal table in the 100 metre freestyle at the 2014 Commonwealth Games in Glasgow, with Magnussen winning gold.

[21] At the 2016 Summer Olympics in Rio, Magnussen won a bronze medal in the 4×100-metre freestyle relay along with his team members behind United States and France.