They were part of a group of nine young people being baptised by pastors from an apostolic church in Muriwo village, in the east of the country.
Police said they were in a river in Mashonaland East province on Tuesday when they got into trouble.
Officers said two women, aged 30 and 34, had been arrested.
Police spokeswoman Charity Charamba said in a statement: "After realising the children were dead, the culprits ran away from the scene but they were later arrested.
"They are being charged with culpable homicide."
She said a four year old boy managed to escape the river and got help from a passer-by who called officers.
"We would like to warn members of the public to desist from engaging in dangerous practices under the guise of freedom of worship," she added.