As the parents of a murdered 7-year-old Bedford-Stuyvesant girl were formally charged with the girl’s death yesterday, child advocates wondered how the city’s child welfare system failed the girl, who allegedly was abused, and the city’s Administration for Children’s Services pledged to begin an agency wide investigation.

Nixzmary Brown’s mother, Nixzaliz Santiago, 27, was arraigned on charges of second-degree manslaughter and child endangerment. Her common-law husband, Cesar Rodriguez, 28, who was convicted of harassment in 2003, was arraigned on charges of second-degree murder, sexual abuse, and child endangerment.

Ms. Santiago allegedly struck Nixzmary, while Mr. Rodriguez is accused of beating, sexually abusing, and killing his stepdaughter, and even keeping her captive in a room with her ankle tied to a chair that was attached to a radiator, law enforcement sources said. He allegedly punished Nixzmary for behavior such as eating a container of yogurt he had purchased for one of her five stepsiblings, law enforcement officials said.

Law enforcement officials said Mr. Rodriguez on Wednesday repeatedly submerged Nixzmary’s head in a water filled bathtub and killed her by striking her head, possibly on the faucet. The medical examiner’s office ruled the death a homicide, by blunt impact injury to the head. Both defendants are being held without bail.

Ms. Santiago found Nixzmary, her eldest daughter, lying face up on the floor, wearing only pajama bottoms, in the rear bedroom of their Bedford-Stuyvesant apartment at about 4:30 a.m. Wednesday, police said. Ms. Santiago ran upstairs to notify a neighbor, and the neighbor followed her back down and called 911. Emergency Medical Service technicians declared Nixzmary dead at the scene. The other five children were taken into custody by the child welfare agency.

What makes the case particularly troubling to child advocates is that officials at Nixzmary’s school, P.S. 256, filed two complaints of possible abuse with the child welfare agency, one of which the agency considered unfounded. The other is still under investigation.

In a letter to the schools chancellor, Joel Klein, a former City Council member, Eva Moskowitz, pointed the finger at school administrators. “Nixzmary was failed first and foremost by her parents,” Ms. Moskowitz, executive director of the Harlem Success Charter Academy, wrote. “But PS 256 bears responsibility too. Clearly the school adopted a compliance approach to the problem, perfunctorily notifying ACS. They did the bare minimum required of them.”

The commissioner of the child welfare agency, John Mattingly, discussed the case at a press conference yesterday. Referring to the complaint still under investigation, Mr. Mattingly said Mr. Rodriguez made follow-up visits and calls to the apartment impossible, but he noted that the agency should have pressed for a search warrant.

“If we had gotten a warrant and gone in, there was a chance we could have gotten the real story from the family members,” Mr. Mattingly said. “The one thing we’re sure of is that was our critical opportunity. People made judgments about whether it was an emergency or not, and those judgments turned out to be wrong.”

Nixzmary’s death occurred on the same day a 2-month-old Brownsville boy, Michael Segarra, died. In that case, Mr. Mattingly said, the family also had a history with the child-welfare agency. The medical examiner’s office said the cause of death in the case was inconclusive as of yesterday.

Child fatalities have been on the rise in the city, according to a September report from the office of the public advocate, Betsy Gotbaum. “Child fatalities jumped from 46 in 2002, to 63 in 2003, to 73 in 2004,” the report said. Her data came from the New York State Central Register of Child Abuse and Neglect, which tracks fatalities of children in the care of the child-welfare agency as well as fatalities of children that were the victim of abuse.

Of the deaths in 2004, the report indicated, close to 75% were homicides or due to accidents, or the cause was not determined. In close to 70% of the 73 cases, the families had dealings with the child-welfare agency. The Administration for Children’s Services commissioner vowed to begin an agency-wide investigation, starting with a review of 9,500 open Brooklyn cases.

Mr. Mattingly said, “We are beginning today initializing a citywide review of every open child protection case in all of our offices. … We are asking managers, supervisors, and caseworkers, along with deputy directors and borough directors, to do a safety check on every family we are involved with right now in the agency. … We believe it is essential that we take our temperature right away on every case that we are involved with.”

The director of Children’s Rights Incorporated, Marcia Lowry, who headed up a successful 1995 class action against the child-welfare agency on behalf of abused children, said that although the system is better, it still needs improvement. “I think we need to take a hard look at this system,” she said. Agency failings that may have contributed to Nixzmary’s death include the “quality of practice, how decisions are made, what services are provided,” she said. In addition, she said, the agency lacks “any real quality review process” of individual cases or of the agency itself.

Gerard McCafferty, the president of one of the providers that has a contract with the child-welfare agency, the Seamen’s Society for Children and Families, said, “You can’t help but wonder, ‘How did people miss this stuff?'”

As the head of an agency that provides foster care services, Mr. McCafferty said it is important to remember in the cases of child abuse, “We’re still talking about human beings making judgment calls.”