The incident occurred yesterday but came to light today when some local people saw the bodies floating in the well in Chakalipeta area.
The deceased were identified as K Nandini (28), K Sai (3) and K Krishna (2).
Police sub-inspector S Surya Prakash said that K Nagedra, Nandini's husband, had had a quarrel with her a few days ago, and he allegedly beat her up on Thursday afternoon.
The same evening she left the house with the two sons.