The drowning unfolded at Lough Enagh on Monday evening when a group of teenagers entered the water at a jetty.
The boys had stopped off at the lough while cycling in the area.
The Police Service of Northern Ireland (PSNI) said officers were called shortly after 6.25pm to reports of a number of people in difficulty in the water.
The Northern Ireland Ambulance Service (NIAS) said a rapid response paramedic, five emergency crews, a hazardous area response team and an ambulance officer were dispatched.
Lough Enagh, near to where the incident took place
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NIAS also tasked the air ambulance to attend the bank holiday Monday incident.
One of the boys was taken from the water but later pronounced dead in hospital.
The body of the second youth was recovered late on Monday night following extensive searches by Foyle Search and Rescue and police divers.
Another male was taken to hospital for treatment for injuries not believed to be life threatening, while three others have been left shocked, police said.
PSNI’s Inspector Brogan said: “Enquiries are ongoing into this incident but we believe, at this stage, that this was a tragic drowning incident.
“Our thoughts are with the families of those affected.”