A 20-year-old father has been arraigned on charges of second-degree murder and manslaughter in the death of his 2-year-old son, who was presumably found dead in New York’s East River this week.

During the arraignment, prosecutors allege the child was alive when he was thrown into the river.

Police said they have video of the father, Arius Williams, when he allegedly threw the child to his death at 11:57 p.m. on May 10.

Video showed his activities before and after the alleged crime, including showing that the child was alive and in the father’s arms on surveillance video immediately prior.

The child was standing, at one point, and then the video shows Williams throw the child over the bridge, then walk in front of a gas station without the child.

Police believe they found the body of Montrell Williams, who had been missing for a month, in the East River on Wednesday.

Authorities are still awaiting a positive identification from the medical examiner.

The father appeared in Bronx Family Court on Monday to answer a warrant for failing to return the boy to the mother, per their custody agreement. He was put in jail by a judge after he failed to disclose the child’s whereabouts.

William’s mother said he took the child from the house — wearing a shirt, diaper, along with a blanket — after the grandmother said they got into an argument.

After he left the area of the bridge, police said Williams went to another family member’s house and would not explain what happened, then he ran away from the family.

Timeline:

The child was supposed to be returned to his mother on May 11, and when he wasn’t, the mother contacted police and went to family court.

Williams had limited contact with family and did not disclose the whereabouts of the child, the complaint said.

Then, on May 28, family court issued an order for the defendant to produce the child, the complaint said.

On June 8, the mother of the child ran into Williams on the street after not having heard from him and desperately trying to get in contact with him, demanded to know where their child was, according to the complaint.

Williams initially refused, then took her to St. Mary’s Park, where he allegedly pulled a knife and threatened the mother, and said he threw the child in the river, according to the complaint.

The mother continued to follow Williams into Manhattan and contacted police.

He was taken into custody on a custodial interference warrant.

The mother of the child was granted an order of protection.

Family struggling to understand why

Williams’ mother and stepfather and another family member were at the arraignment on Thursday night, and audibly gasped and cried when some of the details were read from the complaint.

The tight-knit family of the young father, accused of doing the unthinkable, is struggling to understand why.

“Nobody expected this at all, because he loved his son. I don’t know what drove him to do this,” said the suspect’s step-grandfather, Leroy Burton.

The mystery is so painful and baffling to the family. They say the boy’s father recently seemed like he had begun struggling with mental health issues.

“The baby kept saying ‘Daddy, daddy, daddy.’ That’s what crushes me the most, is that he kept calling him ‘Daddy, daddy.’ He trusted him…he took his life,” the suspect’s aunt, Alicia Williams, said.

The family is remembering Montrell as a sweet and happy toddler.

Once the body recovered Wednesday has been officially identified, the medical examiner will have to determine exactly how the little boy died.

Williams is facing two counts on each charge of second-degree murder and manslaughter because the victim is under the age of 11.