The incident occurred on Thursday when Sita left the house with two minor sons Subhash (2) and Pappu (5).
She threw both the children in the well and went to her uncle's house and informed about it.
Her uncle and other relatives informed police yesterday, following which the body of Subhas was recovered last night and the body of Pappu was taken out today, SHO Khamera police station Babulal said.
He said that the woman, who has been arrested, said that she was angered by her husband Gajendra's alleged illicit relation with a local girl and both of them eloped from their houses on Wednesday.