The mysteries had vexed southeastern Minnesota law enforcement for two decades:

Who abandoned the infant boy whose lifeless body was discovered by four teenage girls on the banks of the Mississippi River downstream of Red Wing in 2003?

And how did another baby's body end up wrapped in a towel and floating in a Red Wing boat harbor four years before that?

A tearful press conference Monday provided some answers in two cases that have haunted Goodhue County investigators for a generation and helped inspire a Minnesota law granting immunity to mothers who safely give up their newborns within a certain time period.

Jennifer Lynn Matter, a 50-year-old woman from rural Red Wing, was arrested and charged Monday with second-degree murder in the 2003 death after law enforcement officials used DNA evidence to link her to the two infants.

According to the criminal complaint, DNA evidence determined that Matter is almost certainly the mother of the baby found on the banks of the river's Lake Pepin in December 2003. The unclothed newborn was lying on the water's edge with his umbilical cord attached and wrapped around the middle of his body.

Matter also has been identified through DNA evidence as the mother of a dead infant girl found wrapped in a towel in the Mississippi River near Red Wing in 1999, though officials did not explain why charges have not been filed in that death.

"Charges may be amended or added at a later time as more evidence comes to light," said Goodhue County Attorney Stephen O'Keefe.

The investigation of the deaths stretched for two decades and included DNA comparisons in 2004 and 2007 that determined the two infants were related. But authorities did not link Matter to the cases until the past year.

In 2020, Goodhue County Sheriff's investigator Jon Huneke took up the cold cases. Using genetic genealogy, law enforcement compared DNA samples and identified the biological father of the infant found in 1999. Further investigations determined Matter was a person of interest.

"For over 20 years the deaths of these innocent babies have haunted our community," Goodhue County Sheriff Marty Kelly said. "The tenacity of several investigators in our office to obtain justice for these babies and the perseverance by our community who assisted us in finding answers have led us here today. We pray today's arrest and charges provide some closure."

An autopsy of the infant found in 2003 determined the full-term boy probably was born alive. The Minnesota Regional Coroner's Office determined homicide as the manner of death although the cause of death was undetermined. The baby had been found with blunt force head injuries, but those may have occurred during the birth, according to the coroner's office.

Matter was charged with two counts in that baby's death: intentional, non-premeditated second-degree murder and unintentional second-degree murder.

Kelly also brought up a 2007 incident in which a baby's body was found near Treasure Island Marina but said law enforcement is "fairly certain" that baby was unrelated to the other two.

"Our DNA has somewhat hit a roadblock" in that investigation, Kelly said.

Huneke and Brittany Carstensen, a BCA special agent, first interviewed Matter two weeks ago. Matter denied being the mother of the baby found in 1999 and declined to provide a DNA sample. Last week, investigators obtained a search warrant and got a DNA sample, which later concluded Matter was almost certainly the biological mother of both infants.

Matter told investigators that in 1999 she was in a bad mental state, according to the criminal complaint.

"She stated that she was in and out of jail, drinking too much, doing a lot of stupid things, and had experienced chaotic life circumstances for a long time," according to the complaint. "She stated that she was not aware that she was pregnant and that when she was on her way to drop off her kids (age 2 and 5) at school and daycare, that she started bleeding. Matter stated that after dropping off the kids that she returned to her home in Red Wing ... and gave birth in the bathroom. Matter stated that the baby was born blue, was not breathing and was not crying, so she freaked out. Matter stated that she knows that she should have gotten help but that her mind was not there."

Matter told investigators she drove the baby to Bay Point Park in the middle of the night, put her in the water near boathouses and walked away.

She also told investigators that with the 2003 baby, she was alone at a public beach when she went into labor.

"Matter stated that it was dark outside, it was cold, that she did not look to see the gender of the child, and that she remembered leaving the baby on the beach before driving away," according to the complaint. Matter later told investigators that the baby "was breathing fine and it may have been crying but she didn't remember it."

The discovery of the infant's body in 1999 inspired, in part, legislation that made Minnesota among the first states to enact a "safe haven" law, in which unharmed newborns up to 7 days old may be left, no questions asked, at a "safe place." Under the law, that includes a hospital, other urgent health care provider or ambulance.

BCA superintendent Drew Evans lauded the use of rapid DNA testing and genetic genealogy in the investigation.

"These kinds of scientific advances that can aid investigations are happening all the time," Evans said. "That is why it is so important to never give up on any unsolved case."