With no sewage plant Gaza’s waste is dumped in the sea or collected in open pools.
Three women, one more than 70 years old, and two boys aged one and two died in the flood.
At least 15 people were injured and scores more are missing, according to Palestinian medics.
At least 25 houses were completely submerged.
Ziad Abu Farya, head of the village council, described the scene as “our tsunami”.
Fadel Kawash, head of the Palestinian water authority, said that the level of sewage in the pool had increased over the past few days, creeping up the earth embankments around the pool until one collapsed, “causing the sewage to pour towards the village”.
Angry residents drove reporters out of the area and mobbed government officials.
Village children clung to wooden doors floating on the putrid waters and rescuers paddled through the village in makeshift boats in search of victims.
Frantic goats and cows, sustenance for the village of Bedouin shepherds, were also pulled to safety.
“We lost everything. Everything was covered by the flood. It’s a disaster,” said Amina Afif, 65, whose small shack was destroyed.
As far back as January 2004, UN aid agencies in the Gaza Strip had warned that the north Gaza sewage treatment facility was operating far beyond its capacity and posed a grave danger to nearby residents.
Designed to serve just 50,000 people, the plant at that time was handling waste from 190,000 Gaza residents.