The incident took place on Thursday when Dharmendra Dongre, a resident of Jaripatka area, suddenly caught hold of his son Shreyas and threw him on the floor. He then kicked him in stomach and chest before throwing him in a water tank at their house, the police said.
On hearing the toddler's cries, family members rescued him and rushed him to Mayo Hospital in the wee hours yesterday but he succumbed to injuries.
Police had initially registered a case of accidental death and launched a probe into the matter.
The accused was arrested late last night and a case under section 302 (murder) was lodged against him at Jaripatka police station.