The flooding at Bright Angel Creek, which flows into the river, happened Saturday afternoon. Torrents of water wiped out footbridges over the creek and significantly altered the landscape, widening the creek bed and creating what appeared to be a new river rapid.
The park service said it was seeking information about more than 20 people who may be missing or unaccounted for after the flood and asked anyone with details about people hiking or camping in the area to get in touch.
It said it was working with the Arizona Department of Public Safety to continue evacuations on Sunday.
"This is a reminder of what a dynamic and active landscape Grand Canyon is," said Jack Schmidt, director of the Centre for Colorado River Studies at Utah State University.
Popular tourist spots including the Bright Angel Campground, Phantom Ranch and parts of the North Kaibab trail remained closed on Sunday while park officials surveyed the damage, the park said.
Rafting trips on the Colorado River also have been halted for now.
More than 60 people were evacuated from Phantom Ranch, which has a historic canteen and dorms, and is a common spot for rafters to get off and on the river.
More evacuations were planned on Sunday, park staff said. No injuries have been reported.
Erica Viola said she was at Bright Angel Campground when the rain started Saturday afternoon, and she and about 50 other hikers watched the creek rise and then debris start to flow by, including what looked like a bunkhouse.
The group was taken by helicopter to safety, ending her adventure two days early, she said.
About 1cm to 2.5cm of rain fell within about 30 minutes in the rocky area where there's a steep drop in elevation, said National Weather Service meteorologist Justin Johndrow in Flagstaff.
"Most of it ran off instantly," Johndrow said.
He said the flooding happened on the north side of the Grand Canyon, where Bright Angel Creek comes from the North Rim down to the Colorado River, dropping around 1828m.
More rain and thunderstorms were possible for the area on Monday.
