Obama flew three hours west of his native Honolulu to Midway Atoll, on the far northwestern tip of the Hawaiian island chain.
The atoll is situated at the heart of Papahanaumokuakea, a vast Pacific marine reserve given protected status by then- president George W Bush in 2006.
Obama recently quadrupled its size to make it the world's largest marine reserve, home to 7,000 marine species, including many endangered birds as well as the Hawaiian monk seal and black coral, which can live for 4,500 years.
All the atoll's 40 inhabitants -- mostly US Fish and Wildlife Service staff -- greeted him.
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Until recently, the area was perhaps best known to military history buffs.
Seventy-four years ago, the Battle of Midway was a decisive naval fight in World War II that turned the tide of the war against Japan.
Obama praised the "courage and perseverance" of the vastly outnumbered American soldiers who repelled Japanese forces. "This is hallowed ground," he said.
Now, he added, protecting the vast ecosystem "allows us to study and research and understand our oceans better than we ever have before."
Since taking office in 2009, he has designated more protected areas than any of his predecessors using the Antiquities Act, signed in 1906 by Theodore Roosevelt, who established the first national monuments.
For the outgoing president, the visit is part of an eight- year effort to put the environment and tackling climate change higher on the political agenda.
Scientists would be able to undertake "critically important" study of climate change in the marine reserve, he said.
Although Bush created Papahanaumokuakea, he also earned international scorn by rejecting the global climate deal reached at Kyoto.