The deceased have been identified as Hemachandra, B Lokesh, both are 9th standard student, and B Rajesh, an 8th standard student, police said adding Lokesh and Rajesh are brothers.
The incident occurred yesterday when the trio, along with two others, went to the bank of Nagavali river after school hours to play, they said.
After playing there till dusk, they all went into the river to take a bath, following which the victims disappeared, they said.
Upon hearing the other two students' cries for help, a woman rushed to the spot and informed some teachers of a nearby school, they said.
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Superintendent of Police A S Khan gave the necessary directions for the rescue operations, they said.
The District Fire Officer M Srinivas Reddy and the Revenue Divisional Officer B Dayanidhi were also present until the bodies were sent for post-mortem to the Rajiv Gandhi Institute of Medical Sciences here, they said.
Srikakulam MLA Gunda Lakshmi Devi visited the spot and condoled the deaths, they said.