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The young girl was brought to the Healdsburg Police Department that night and was unresponsive, according to police.
Healdsburg police are investigating to figure out how and why this tragedy occurred.
There was no Mass on Monday while officials investigate the crime scene at Healdsburg's St John's Catholic Church.
"We do believe she was drowned and that it was intentional," Healdsburg Police Department Chief Kevin Burke said.
Burke explained why detectives arrested 42-year-old Gerardo Mendoza Ordaz and charged him with the death of his daughter. Police say Ordaz showed up behind the police station Sunday night, naked, and crying for help as he held his unconscious daughter with his son by their side.
"We are relying on testimony of the older son and the statement of the suspect," Burke said.
It is Healdsburg's first murder since 2008.
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Family and friends were surprised and sad when they learned the news.
The young girl remains unidentified at this time.
Neighbors say she was a sweet little girl.
As to how this could happen in a church? "They were the only people inside the church at the time. There were no other parties present. As I understand it our local Catholic church, leaves the doors to the premises unlocked late on Sundays. And so they were in there alone at the time through an unlocked door," Burke said.
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The Santa Rosa archdiocese and St. Johns Catholic Church did not release a comment on Monday.