The father called 911 after he arrived at the home of his wife, Genevieve Ellen Springer, on Saturday morning in Murphy, according to the Cherokee County Sheriff's Office.
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The couple were separated, so the father went to the home for a custody exchange.
Authorities are trying to determine when the children died. The father, who was not named by authorities, said he last saw them alive Feb. 26.
A statement by the Cherokee County Sheriff's Office said an autopsy will be performed on the victims that should help determine when they died.
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Springer has been charged with two counts of first-degree murder and was being held without bond in the Cherokee County Detention Center.
The sheriff's office said she was briefly hospitalized in North Georgia and arrested Saturday in Union County, Georgia, upon her release.
In the statement about the slayings, Cherokee County Sheriff Dustin Smith asked for prayers for the victims' family, friends, and the first responders involved in the incident.
The Associated Press contributed.