Residents of Ganderbal area in central Kashmir claimed Tariq Ahmad Bhat and two others jumped into the river when they were chased by security forces, the Economic Times reported.
A police spokesman denied the allegation, saying the youth drowned after a boat capsized on the river.
One youth managed to swim ashore, residents said adding another was saved by some persons.
However, Bhat could not be saved and his body was later fished out, they said.
The death of youth led to fresh protests in the area. The police spokesman said six persons were injured in Watergam area of Baramulla district while "tackling" law and order situation.
He said two of the injured were critical and rushed to SKIMS hospital here for treatment while three were admitted to Baramulla district hospital.
The spokesman said one of the injured had been discharged after the first aid.
Although he did not elaborate on how the youths were injured, the residents alleged that security forces opened unprovoked firing on the protesters.
Sporadic protests were also reported from some parts of Srinagar city and south Kashmir Kulgam district.
However, there were no reports of anyone getting injured in the clashes with the security forces.
Mohammed Afzal Guru, convicted of involvement in the audacious attack on Parliament in 2001, was hanged yesterday and buried in Delhi's Tihar Jail.