Jayveyon Burley, 22, was also charged with assault on a child causing death. He made a brief court appearance at the Long Beach Courthouse Wednesday, but his arraignment was postponed until Jan. 10, according to the District Attorney's Office.
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On Sunday, Burley picked up his 3-year-old son and his 1-year-old daughter, Leilani Dream Burley, from their mother's home in Long Beach, prosecutors said.
The girl's grandmother called police that evening when her son, who lives with her, returned home with only the boy, authorities said.
RELATED: Police arrest Inglewood father after baby girl's body found in Los Angeles River in Long Beach
Police arrest Inglewood father after baby girl's body found in Los Angeles River in Long Beach
Police began a search for the missing girl. Her body was found Monday in the Los Angeles River at the river's southern end in Long Beach, authorities said.
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Police didn't immediately release the specific cause of her death or whether she was dead before she was thrown into the river.
Burley was arrested Monday. His bail has been set at more than $2 million.
"My daughter was murdered by her father," Lynisha Hull told Eyewitness News earlier this week. "He threw her off the bridge."
Hull said Burley normally picks up both their children on Sunday nights and returns them to her on Wednesdays.
He was angry at the time he picked them up but didn't say or do anything that would foreshadow what he was then accused of doing, Hull said.
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"He came to my home to pick up my kids," she said. "He was angry at the time but normal though. He was normal. He didn't look like he was panicked at the time at all."
A GoFundMe page has been established to help the victim's family with funeral expenses.
City News Service and the Associated Press contributed to this report.