Investigators say in a release that they believe they have enough evidence to show the death was premeditated.
The boy was pronounced dead in hospital Tuesday.
He had been taken there after EMS personnel were called to an apartment on the city's south side.
Results of an autopsy have not been released, although police at one point said the boy appeared to have drowned.
Nerlin Sarmiento, who is 32, is to appear in court Friday.