Ricardo Santiago, 34, of Millville, was charged after surrendering on Tuesday night, police in Vineland, New Jersey say. He is being held on $1 million cash bail.
Also Tuesday night, the bodies of 34-year-old Neidy Ramirez and her daughter, Genesis, were recovered.
Police say Santiago led officers to the bodies, which were found at a boat ramp at 666 Back Neck Road in a rural part of Fairfield Township, Cumberland County.
While the motive remains under investigation, police appear to have some indication as to what happened.
"They were co-parents and it appears there was some sort of dispute," said Lt. Matthew Finley of Vineland City police.
Investigators did not say if there were any obvious signs of trauma. The New Jersey State Police Crime Scene Unit is on location.
Police said the family of the victims, including baby Genesis' biological father, have been notified.
Neidy Ramirez had two other children, a 5-year-old and an 8-year-old. Police said Santiago is the father of the 5-year-old. Those children are now with family members.
Vineland police say Neidy and Genesis spent time with family on Thanksgiving, and they were last seen at a laundromat on Friday.
On Saturday, a coworker found Ramirez's abandoned 2005 Chevy Trailblazer on northbound Route 55 near milepost 45.3.
When Ramirez didn't show up for work Monday morning, the friend informed others. The family went to Route 55, saw the vehicle, and immediately called police.
Stephanie Joynes, who worked with Ramirez at Conte's Pasta, said "We knew that there was some kind of custody issues going on, but we didn't know half of it."
Joynes said that when Ramirez didn't show up for work on Monday, everyone knew something was wrong.
"She was always good about calling us if she was going to be late or if she wasn't going to be here," Joynes said.
The store was closed for a short time on Wednesday to give employees some time after they found out Ramirez, and her baby girl, were gone.
"We're all just trying to get through the day so we can focus on the family," Joynes said.
As the investigation continues, Vineland police ask anyone with information is asked to call them at 856-691-4111 x4180 or the Cumberland County Prosecutor's Office at 856-453-0486.