Police say she took them to the Murray River and tried to drown her oldest son.
The body of a five-year-old boy feared drowned has been found in the Murray River in New South Wales after his mother was charged with attempted murder of her other son and a court heard she "had to drown my babies".
At 10pm, their mother, who can not be identified for legal reasons, presented herself to a police station in Echuca on the Victorian side of the river.
The dead boy's mother, who can not be identified for legal reasons, is facing an attempted murder charge in relation to her other son, who is nine-years-old.
Detective Sergeant Trent Swinton told the court that the mother was attempting to drown her nine-year-old when screaming from his younger brother, who was standing on the riverbank nearby, distracted her and allowed the older boy to escape.
She was charged on Friday night and will appear in court for a bail hearing on Saturday morning.
The woman, 27, from Deniliquin, sobbed uncontrollably as she faced Bendigo Magistrates Court via video link just after 4.30pm on Friday afternoon.
Police said the boy's nine-year-old brother remains in a stable condition in hospital in Melbourne.
The father of the boys has spoken of his devastation and said he was numb after learning about what had happened.
NSW police confirmed she would face further charges during a court appearance on Monday.
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The woman's eldest boy, 9, survived after a dog intervened and attacked her.
"The dog is four years old and it's never attacked one person, has grown up with kids, and it's always been around kinds playing", one told the Herald Sun.
Lawyer Dale Brooks, representing the woman's mum who had been helping to care for the boys, said she is an "ice" or crystal meth addict who is well-known to authorities. He was last seen floating face-down in the river. The court heard how she allegedly told witnesses the night before the incident that she "had to drown my babies". "She's confused and she's upset", he told reporters.
The older boy was then "savagely mauled" by a dog.
The 27-year-old mother with a troubled history seems more known about than really known in the town of 8000 people.
The daughter then "snatched" the children in the grandmother's auto.
"Without any communication by your office (or police) or agreement from our client, (she) was released from jail. and taken to our client's home with no regard for the AVO in place protecting our client", it read.
"It will rock the community of Australia", he said. And the child (in hospital) has lost his mother and probably his brother, it will change his life forever. "The actual circumstances are unknown", Supt Condon said.
The couple had taken out an apprehended violence order against their own daughter in May a year ago, which required that she not "assault, molest, harass, threaten or otherwise interfere with" her mother, as well as orders that she should not approach her mother within 24 hours of consuming liquor or illicit drugs.
Victorian Police divers have also been searching the river.