The sisters from war-torn Sudan, who were 9, 11 and 17 years old, are the latest known victims of a Mediterranean migration route that has claimed more than 30,000 lives since the International Organisation for Migration started counting in 2014.
Volunteers with the German group RESQSHIP found their bodies after rescuing some 65 people from the unseaworthy boat in international waters north of Libya on the night of Friday to Saturday.
The sisters' mother and brother were among survivors who were brought to shore on the Italian island of Lampedusa late on Saturday, the group said.
The green rubber dinghy had departed Zuwara in western Libya earlier Friday.
"The boat was really overcrowded and partially deflated," Barbara Satore, one of the rescuers, told The Associated Press.
"It was a really pitch dark night with 1.5 metre waves, and the boat had been taking on water for hours."
Satore said they found it after an alert from a special network, which receives calls from migrant boats in distress.
It was only after rescuers evacuated around two-thirds of the people on board that the bodies emerged floating in a pool of water and fuel at the bottom of the boat.
"I heard a woman screaming and a man pointing into the water," Satore said.
The darkness and weather conditions made the rescue very dangerous, she added.
"The medical team attempted resuscitation, but they had been underwater for an extended period of time."
The mother remained in shock and sat next to the remains of her daughters aboard the rescue ship, Satore said.
Relatives asked the crew for white sheets and wrapped the bodies with them.
Among the other people rescued were pregnant women and many children, Satore said.
Four of them required urgent medical evacuation and were transferred to an Italian coast guard vessel alongside their family members.
Survivors came from Sudan, Mali, the Ivory Coast, Ethiopia and Eritrea, she added.
5°C