Logan Mwangi, also known as Logan Williamson, was found in the River Ogmore in Aberkenfig on Saturday.
John Cole, 39, has been charged with murder. He, Angharad Williamson, 30, and a boy, 13, are also charged with perverting the course of justice.
Mr Cole and Ms Williamson, both from Sarn, and the teenager appeared at Cardiff Magistrates’ Court.
In a separate hearing earlier on Thursday, Mr Cole spoke only to confirm his name and age. He was remanded in custody and will go before Newport Crown Court on Friday.
Angharad Williamson, 30, also from Sarn, and the 13-year-old boy, who cannot be named because of his age, appeared in a separate hearing, charged with perverting the course of justice.
Logan’s body was found after reports of concerns for a missing five-year-old in the early hours of Saturday.
Logan was found in the river at about 05:45 BST and was taken to Princess of Wales Hospital in Bridgend where it was confirmed he had died.
One of Logan’s classmates, who came with her parents to pay tribute near where his body was found, described him as a “happy boy” who “liked Spider-Man” and “playing hide and seek”.
The girl’s mother said: “He just seemed really happy and a good boy. He was in my daughter’s class for two years I think and they would be going up to big school in September.”
Logan’s neighbour Teresa Mason said: “The boy was really sweet. A happy-go-lucky child.
“We can’t get our heads around it. We normally see him running around here with other kids. We got up Saturday and there was police outside the house. It’s just shocking.”