The bodies were recovered from the Thengar Char Island early on Friday, said Hatia Police OC Md Abul Khair.
The dead have been identified as 12-year-old Razib Uddin and 13-year-old Insan Ullah, both from Purba Gamchhagali village in Char Ishwar, an islet.
As many as 10 fishermen and two children went fishing in the river on a boat, owned by Char Ishwar Union Parishad member Selim, OC Abul Khair said.
“At one point, the boat sank in the river late at night due to high tide. The fishermen managed to swim ashore but the children were trapped.”
The locals recovered the bodies in the morning and police handed them over to their families.