The deceased was identified as Shakib Hossain, 10, a class III student of Swaruppur Government Primary School and son of Alamgir Hossain of Sadar upazila in Chuadanga district.
SM Enamul Haque, officer-in-charge of Chowgachha Police Station, said Shakib used to live at his maternal grandmother house.
Quoting family members, police said Shakib had gone out from him home on Sunday evening and since then he did not return home.
Local people spotted the body of Shakib at the water body near his school and informed the matter to police who recovered the body around 10 am.
Miscreants might have killed the boy brutally and dumped the body here, said OC. The right eye of the boy was also found gouged out, he added.
The motive behind the killing could not be known immediately.