Saturday's flash flood severely damaged the only water pipeline into the canyon.
Officials barred tourists from staying at lodges and hotels inside Grand Canyon National Park and issued emergency water restrictions for year-round residents.
Waves of rain hit the Bright Angel Creek area of the tourist destination that hosts 4.4 million visitors a year.
About 80 people were rescued during the flooding. Officials are seeking information on one person who remains missing.
Incident commander Dave Black said officials used night vision and other equipment to find people who needed to be evacuated over the weekend.
Rangers used the park's permit system and checked vehicle licence plates to track the number of missing people.
There could be day hikers who didn't get permits and therefore weren't recorded as missing by the park, Grand Canyon Deputy Superintendent Brian Drapeaux said.
The flood happened deep in the canyon near where the Colorado River flows, around popular lodges and camping areas where people hiking from one rim of the Grand Canyon to the other stop for the night.
Scores of visitors had to be evacuated from the area by helicopter. They talked of a massive deluge and rangers warning of rockslides, and saw huge pools of logs and debris rolling down the river as they stood nearby awaiting rescue.
The family of John Giusti, 53, said the Texas chiropractor set out on Thursday on a trip he dreamed of with two buddies - Texas martial arts studio owner Brent Rosenkranz, 42, and Wyoming pilot Timothy Smith, 53. They planned to spend two nights at the bottom of the canyon fishing and hiking.
They spoke to their families on Thursday and found their campsite on Friday. They have not been heard from since, the three families said in a joint statement.
Their families said they planned "several days of hiking, camping, fishing and exploring together."
Park officials said they recovered the body of a 46-year-old man on Sunday evening near Crystal Rapids along the Colorado River and were trying to recover a second body.
Shannon Cahill said her brother and his daughter were missing somewhere in the Grand Canyon region.
Michael Wilhoit, 53, Mystic Wilhoit, 30, and her boyfriend left on Saturday for a three-night camping trip. She hasn't heard from any of them since. Phone calls go straight to their voicemail, and they have not posted on social media.
"That's not like Mystic. If she's doing something, she's posting. She posts constantly," Cahill said.
Late on Monday morning, more rain fell as the state Department of Emergency and Military Affairs was co-ordinating with the park service and county emergency management officials in search and recovery efforts.
Visiting the Grand Canyon can be particularly dangerous in the summer because of the risk of flash flooding that accompanies the rainy season.
Clear days can quickly give way to thunderstorms and downpours. Forecasters warned more flooding could happen on Monday.
The flood was a major blow to an enduring effort to modernise the water pipeline that serves visitors and the roughly 1600 residents of Grand Canyon Village.
A $US208 million ($A290 million) rehabilitation of the pipeline and upgrades to the associated water delivery system started in 2023, to ensure the park can meet the needs of residents and visitors.
