Police have identified the deceased as Shivam (14) and the accused as Sonu alias Mangal (35) and Aakash (20) - all from Chandasmad village under Khatauli police station in Muzaffarnagar district.
According to the police spokesperson, Shivam, who was a student of Maharshi Dayanand Inter College Pilona, had left home for his college on January 8 but did not return.
After Shivam's kin and his father Nawab Singh could not locate him they filed a police complaint.
Looking in to the CCTV footage, installed in the village by the Nagar Panchayat, the police took the two accused in custody and interrogated them, the spokesperson said.
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The two confessed to have murdured Shivam and dump his body in the Ganga river, he said.
He said that based on the information provided by the accused, the police recovered the body from the river near Makhdumpur.
The accused told police that they murdured Shivam as they had a scuffle with him few days, the spokesman said.
They threw his school bag in Khatauli canal, which was also recovered.