Gila County sheriff's Lt. Virgil Dodd said the first body found was of a 5-year-old boy. The second child's age and gender weren't provided in a statement released by the Sheriff's Office.
Dodd said the 5-year-old boy's body was found about 3 miles (4.8 kilometers) downstream of the crossing which had been closed hours before the truck tried to cross Friday despite barricades and warning signs.
Drivers "really need to not ignore that. It's very dangerous. It's very hazardous," Dodd said in announcing the first death. "In this case, this horrible and tragic incident ... that's what happens when you ignore these types of signs."
The Sheriff's Office said emergency personnel and law enforcement helicopters on Friday rescued two adults and two children who also were in the military-style truck swept downstream in Tonto Creek near the small community of Tonto Basin, which is about 52 miles (83 kilometers) northeast of Phoenix.
Sheriff's officials previously said a total of six people, including four children, were rescued Friday at locations along the creek.
The people in the truck didn't live locally, Dodd said, but he didn't know the relationship between the adults and the children.
"We have no information as to why they were trying to cross the creek," Dodd said. "We think everybody was in the cab at the time."
Rescue teams from multiple agencies participated in the search, and authorities brought in a bulldozer to pull the truck from the creek bed Saturday.
"Searchers found the truck about 1,000 yards (around 914 meters) downstream from the crossing Friday night," Dodd said. "There was nobody in the truck."
Adverse conditions included heavy brush and slippery mud along the creek and frigid water from snowmelt, but officials said they remained hopeful.
Sheriff's Deputy Phil Smith said the creek only flows during storm runoff.
A National Weather Service meteorologist said the agency issued a flood warning for the region that includes the Tonto Basin area at 8:53 a.m. Friday based on data from an upstream flooding gauge.
Meteorologist Sean Benedict in Phoenix estimated that up to 2 inches (5 centimeters) of rain fell in the area, with some of the runoff coming from snow that fell on nearby peaks.
The region got up to 4 inches (10 centimeters) of rain about a week before, Benedict said. "So the grounds were already pretty wet and that probably helped with the runoff."