The deputies were able to escape, but the two women were not. The women weren't identified.
The incident has spawned investigations by the State Law Enforcement Division and Highway Patrol.
A woman who answered the phone at a number listed for Flood told a reporter he didn't want to talk to anyone.
According to CNN affiliate WPDE, the women were being transported from a hospital in Loris and from the Waccamaw Center for Mental Health in Conway to McLeod Health Darlington, Fox said.
The Lumber River as of September 19 was still in "major" flood stage in several places, according to the National Weather Service.
The Little Pee Dee River reached major flood stage after Hurricane Florence battered the Carolinas over the weekend and is expected to crest at 16 feet on September 21, seven feet higher than flood stage.
I-95, which goes from Maine to Florida, travels through low-lying plains in eastern South and North Carolina.
Thompson said he did not believe the women were in restraints in the back of the van.
The death toll from Hurricane Florence climbed to at least 37, and North Carolina's governor pleaded with thousands of evacuees not to return home just yet.
Cooper warned that the flooding is far from over and will get worse in places.
"I know for many people this feels like a nightmare that just won't end", he said.
President Donald Trump, meanwhile, arrived in storm-ravaged North Carolina on Wednesday and helped volunteers at a church in the hard-hit coastal town of New Bern.
There are widespread road closures due to flooding on primary and secondary routes throughout the Pee Dee, according to the SCDOT.
"Tonight's incident is a tragedy".
The bodies of the two women were recovered on Wednesday, almost 24 hours after the event began, from the submerged van in the Little Pee Dee River.
According to statute, the documents authorizing the admission require "a law enforcement officer, preferably in civilian clothes and preferably with crisis intervention training, to take into custody and transport the person to the hospital designated by the certification". "Floodwater rose rapidly and the deputies were unable to open the doors to reach the individuals in the van".
Rescue crews needed about 45 minutes to find the van, which was under water at that point, and plucked the Horry County deputies from the roof, the sheriff said.
Because of darkness, responders decided trying to retrieve the women's bodies from the van Tuesday night wasn't safe.
The Marion County Coroner has confirmed the deaths of both detainees, who have not been identified.