WORCESTER — The mother whose squalid Blackstone home was found to contain the remains of two infants and a fetus has been indicted on two murder charges, while the father appeared in court Tuesday to face several serious child abuse charges.

Erika L. Murray, 31, was charged in the deaths of two infants who were found in a closet, wearing diapers and onesies, Worcester District Attorney Joseph D. Early Jr. said. Murray, who has been held on $1 million bail since September, did not appear in court Tuesday.

The charges against Murray’s live-in boyfriend, Raymond Rivera, 38, focused on two young children found in the home.

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Authorities described the children as profoundly neglected.

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Rivera had tearfully told reporters last month that he had been banished to the basement by Murray and had no idea of the deteriorating condition of the upper floors, or even the existence of the 3-year-old and 6-month-old girls.

But a prosecutor on Tuesday said that Rivera had slept in a room with Murray “only 7 or 8 feet from where the children were confined,” and that he must have heard the 6-month-old infant constantly crying and the 3-year-old banging on the door.

“There is simply no way he did not know,” Assistant District Attorney John E. Bradley Jr. said in Worcester Superior Court Tuesday.

In August, authorities found four living children in the home on St. Paul Street in Blackstone, including a 3-year-old girl authorities said was unable to walk, talk, or hold utensils, and a 6-month-old girl they described as similarly neglected.

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Police returned to the home in September, armed with search warrants, and discovered the remains of the two infants and the fetus.

Rivera bowed his head and trembled Tuesday during the brief proceedings before Judge James Lemire in Worcester Superior Court.

He pleaded not guilty to two counts of assault and battery on a child, and two counts of reckless endangerment of a child, among other charges, and was ordered held on $100,000 bail.

AP Photo/Telegram & Gazette, Rick Cinclair Raymond Rivera.

Rivera faces up to 30 years in prison if convicted of both charges of assault and battery on a child, prosecutors said.

Nicole Longton, Rivera’s attorney, said he has deep roots in the community and has cooperated with police in their investigation.

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She said that Rivera had not realized he was the father of all seven children until a DNA testing result became known.

“He looks forward to answering the charges,” she said.

Longton said that the two oldest children, a 13-year-old girl and a 10-year-old boy, both of whom had attended school, were now in the care of Rivera’s mother.

Early said the two younger children are in the custody of the state Department of Children and Families. “They are clean and well-fed and doing well,” he said of the younger children.

At Rivera’s arraignment, Bradley said the house “was filthy beyond belief.’’

“There was feces in the walls, soiled diapers pile a foot high,” Bradley told the court. “Upstairs looked like a landfill with garbage and trash piles.”

At a press conference, Early was asked how such unthinkable horror could have gone on, undetected, for so long.

It wasn’t until a neighbor lodged a complaint about a crying child that police entered the trash-filled, flea-infested residence and found the four children, the youngest two of whom were allegedly never taken outside.

“The are a lot of rational questions without rational answers,” a grim-looking Early said. “Everyone who went into that house said they had never seen anything like it.”

“It was unimaginable,” he said.

Besides the two counts of murder, Murray was charged with concealment of fetal remains, which was found with its placenta still attached. She was also indicted on two counts of assault and battery on a child with substantial injuries, two counts of reckless endangerment of a child, and two counts of animal cruelty.

She is due in Worcester Superior Court on Dec. 29 to face the charges.

She previously pleaded to not guilty in Uxbridge District Court to charges of concealing fetal death, permitting substantial injury to a child, witness intimidation, and animal cruelty.

“I’ve never seen anything like this,” Early told reporters. “This case is unique in a lot of sad ways.”

More coverage of the Blackstone case:

Laura Crimaldi and Patricia Wen of the Globe staff contributed to this report. Sean P. Murphy can be reached at smurphy@globe.com . Follow him on Twitter @spmurphyboston