Police say Ashlee Hutt and Mac Leroy McIver were found living with three children, aged six, four and two, among rat droppings, drug needles and heroin.
Ms Hutt appeared in court on Monday and faces child endangerment charges. Mr McIver faces similar charges.
The three children were removed from the home last November.
The couple deny the charges against them.
Pierce County Sheriff's Department spokesman Ed Troyer told The Washington Post: "The kids lived in deplorable conditions. It wasn't a good living situation even without the issue of heroin."
According to court documents, the six-year-old told investigators the couple gave him "feel good medicine" which he described "as white powder which was mixed with water" and injected with needles.
He said after they were injected the three children would go to sleep.
Two of the children tested positive for the drug, and puncture marks and bruising, consistent with needle injections were also found on the children's bodies, according to reports.
Both Ms Hutt and Mr McIver have pleaded not guilty to the charges, though they both admitted to being heroin users.
In September, Ohio police released a graphic photo of a couple overdosing on heroin with a boy in the car to raise awareness of the state's heroin problem.
The US is in the throes of a heroin and opioid epidemic - drug overdose has become the leading cause of accidental death, overtaking traffic accidents.
A young couple in the US state of Washington are accused of injecting three young children with heroin to "make them go to sleep".