A 43-year-old woman told police the children were her adopted daughters and had been frozen since February.
The remains were found by authorities investigating reports of child abuse at the address.
The county sheriff's office told the BBC the woman was arrested and was being held without bail.
The authorities visited the house, in Lusby, on Saturday to investigate reports of abuse against a third child, a seven-year-old girl, who showed "signs of extreme abuse and neglect", the sheriff's department said.
When police arrived at her house to look for evidence of the alleged abuse, they found the children's remains in a chest-style freezer.
The woman said that the remains were those of her adopted children and had been in the freezer since she had moved to the area in February, said police.
She also admitted to hitting the seven-year-old with a "hard-heeled shoe".
"It's a tragedy, and it gets to you a little bit," County Sheriff Mike Evans told a news conference on Monday.
"You think you've seen it all, but you haven't."
Police confirmed that the woman had adopted three children but that they had not yet been able to examine and identify the bodies.
The woman has been charged with first degree child abuse and is being held in a county jail without bail.Just how sick is that? Where is this world going?
