Prosecutors had charged Amanda Hamm, 30, with first-degree murder in the deaths of Christopher Hamm, 6, Austin Brown, 3, and Kyleigh Hamm, 1.
Authorities said Hamm was going along with her boyfriend's plan to drown the children to get rid of the strain they added to the couple's sometimes abusive relationship.
Maurice LaGrone, now Hamm's ex-boyfriend, was convicted in April of murdering the children and is serving a life sentence without the possibility of parole.
Hamm showed no emotion as the verdict was read, but began sobbing after the jury left the courtroom. Her attorney, Steve Skelton, held her head in his hands.
Relatives of Hamm and the children also cried.
Skelton said the verdict means the jury decided Hamm did not help plan murders, but should have known LaGrone was a threat to her children.
Jurors deliberated 27 hours over five days to reach the verdict, which carries a sentence ranging from probation to 20 years in prison. Hamm has been jailed for three years.
Craig Brown, Austin Brown's father and another former boyfriend of Hamm's, said the verdict would make it difficult for the family to find closure.
"Nothing's going to bring them back, but to let her walk out of there like that is a bunch of crap," Brown said.
Sentencing was set for Feb. 1, and her bond was reduced to $100,000, from $5 million.