The arrest of the nuns --Ramya and Maria Thankam-- who runs the daycare, which is part of a convent, and helper Kunjamma, comes two days after one-and-a-half year-old Adhav went missing from the centre and found dead in the River Periyar.
Police said they have been charged under section 304(A) (causing death by negligence) of the IPC.
The toddler was dropped by his parents at the daycare on Wednesday when he was found dead in the river, flowing just 50-100 meters away from there.
The kid who walked towards the river shore might have accidentally fallen into the water, police said.