Huge breakers pummelled the US garrison at Kwajalein Atoll last weekend on Roi-Namur island, where some of America's most sophisticated space and missile tracking equipment is housed.
Video footage from inside the garrison showed surging water from the waves knocked over bystanders, smashed open glass doors and shattered windows.
Around 80 of the 120 personnel had to be evacuated, the US military said, and a 60-strong team was assessing damage and restoring basic services.
Aerial photos showed extensive damage to the island's infrastructure after the waves left several areas underwater.
"Clearing the runway on Roi-Namur and assessing its safety is our top priority," garrison commander Colonel Drew Morgan said in a statement.
"Once the runway is open, we can move people and equipment back and forth to start the recovery process."
It could take months to fix the damaged garrison, the US Army said, after seawater swamped the accommodation, dining, transport and entertainment buildings.
The Marshall Islands are a sprawling chain of volcanic islands and coral atolls halfway between Hawaii and Australia.
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