The woman, identified as Geetha (40),has been admitted at the District hospital in Kanhangad with injuries, they said.
Family dispute is reportedly the reason for the woman, a private school teacher, taking the extreme step.
Her husband, a newspaper vendor, had gone out on work early this morning, but could not find his children, Harinanda (6), Lakshminanda (3) or his wife at home on his return.
While searching for them, he heard a noise from the well which had eight feet depth of water. He found his wife perched on a foot step on the wall of the well, they said.
The body of the elder child was recovered later.