Authorities did not disclose a motive for the slaying, but the Marine, 20-year-old Robert Quiroz, told a TV station in September that he felt overwhelmed as a single parent of two and struggled to accept his son.
"I didn't know how to feel about him. The same day he was born, my wife died," he told KMPH in Fresno. "The feelings inside of me, I kind of wanted to push him away, but he's my son. My wife gave him to me."
Quiroz was jailed on Monday. Investigators said his son died of beating injuries, but they would not elaborate. Authorities planned to file charges Wednesday.
After the infant's death on Saturday, authorities took Quiroz's 18-month-old daughter into protective custody.
In August, Quiroz deployed to a training camp in Kuwait with the Ninth Communication Battalion from Camp Pendleton. He was called home three days later with the news that his wife had given birth to a boy, but had suffered an aneurysm after breast feeding the child.
Quiroz arrived in Fresno faced with ending her life support and assuming sole responsibility for their two children.
"This is an absolute tragedy," Police Chief Jerry Dyer said. "When you consider the fact that we have a 3-month-old child that has been murdered, it takes a toll."
Quiroz's Web page on MySpace.com, posted under the screen name "IMISSHER," appears to have been an outlet for his loss.
"On August 21, 2006, my whole world ended. For those of you who don't know, my beautiful wife Candice died," reads Quiroz's site. "Just because you see me smile and you see me laugh doesn't come close to the way I feel inside. I will never be as happy as I was until I'm with my wife again."
After his wife's death, Quiroz was permanently transferred to the Fresno-based Marine Reserve Training Center. He moved in with his sister-in-law and her boyfriend, who helped him look after the children.
"With these two kids, they're a handful," Quiroz said in the television report. "It's ... really hard right now."
At the training center, Quiroz was assigned to sort toys for holiday donations and other administrative duties.
"He was quiet," said Maj. Timothy Rizner. "Like a good Marine, you'd tell him to get mission accomplished and he'd go off and do it."
Police had started a child abuse investigation in October after Quiroz's son was hospitalized for a broken arm. The infant was placed in protective custody, but the county Department of Children and Family Services released him to his father after a few days, police said.
Child welfare officials said they would investigate why the baby was returned to his father.
"This has absolutely devastated this department," said Catherine Huerta, the department's acting director. "Our job is to protect kids, and when something like this happens, it's a failure."