The counts stem from two incidents involving a 27-year-old woman -- identified by Phoenix police Sgt. Trent Crump as Dwyer's wife -- and an 18-month-old child at Dwyer's home in southeast Phoenix on July 21 at 8 a.m. and July 22 at 4 p.m., according to the Phoenix Police Department.
Dwyer, 25, was booked into Maricopa County Jail on Wednesday on one count of aggravated assault causing a fracture, one count of aggravated assault involving a minor, two counts of criminal damage, one count of preventing the use of a phone in an emergency, and assault.
He was freed on a $25,000 cash bond early Thursday and ordered to wear an electronic monitoring device. He also cannot have contact with the alleged victims, cannot travel outside of Arizona and cannot have involvement with weapons, drugs or alcohol.
Dwyer admitted to the incidents during interviews with detectives but denied physically assaulting the female and child. According to police, a search warrant was being executed at his home.
According to a statement, the Cardinals weren't made aware of the allegations against Dwyer until Wednesday but are fully cooperating.
"Given the serious nature of the allegations we have taken the immediate step to deactivate Jonathan from all team activities," the team said. "We will continue to closely monitor this as it develops and evaluate additional information as it becomes available."
An NFL spokesperson said Dwyer's arrest will be reviewed under the league's personal conduct policy.
According to Phoenix police, Dwyer's wife and child left Arizona shortly after the July incidents, but a report wasn't filed with the Phoenix Police Department until Sept. 11. After conducting interviews with witnesses and obtaining out-of-state medical records, investigators developed probable cause to arrest Dwyer on Wednesday in Tempe, Arizona.
Authorities depicted a stormy relationship between Dwyer and his wife that escalated into violence on July 21, four days before the Cardinals reported to training camp.
Neighbors heard a fight and called police, who showed up at the residence but left without making an arrest because Dwyer hid in the bathroom and his wife said no one else was at the home, Crump said.
"She said she was in an argument on the phone only," Crump said.
The next day, Crump said, Dwyer snatched his wife's cellphone and threw it from the second floor of their residence to prevent her from calling police about another dispute.
Crump confirmed there was an allegation that Dwyer threw a shoe at or toward his son. Crump said he couldn't elaborate on it.
Crump said the wife moved out of state with the child but came forward last week and provided police with information about her injuries and text messages indicating Dwyer "was going to harm himself because of what had been going on."
This is the second domestic violence case involving a Cardinals player. In April, inside linebacker Daryl Washington pleaded guilty to assaulting his ex-girlfriend and is serving a year of supervised probation. Washington has not yet been penalized by the NFL for the offense but is suspended for this season for violating the league's substance abuse policy.
The Maricopa County Sheriff's Office, which runs the jail, said Dwyer had refused all media interviews.
Dwyer was signed on March 12 to a one-year contract as a free agent. He was scheduled to be the Cardinals' highest-paid running back at $795,000 this season, according to ESPN Stats & Information. Through two games, Dwyer was the team's second-leading rusher with 16 carries for 51 yards and a touchdown.
The Cardinals are now left with two healthy running backs and an injured starter heading into Sunday's game against the 49ers.
Starting running back Andre Ellington missed Wednesday's practice as he continues to recover from a torn tendon in his left foot. The two healthy running backs -- Stepfan Taylor and Robert Hughes -- have combined for two carries for 4 yards this season as Arizona's third and fourth options.
As of Wednesday evening, Chris Rainey was the only running back on the Cardinals' practice squad. Rainey was waived by the Steelers in 2013 after being accused of slapping his girlfriend. Rainey also pleaded guilty to a misdemeanor stalking charge while in college at Florida, according to reports.
The Associated Press contributed to this report.