Residents attempted to dig trenches to direct the water from flooding their tents, as rain dripped through tears in tarpaulins and makeshift shelters.
The first rain of the season pounded down in intermittent bursts, soaking the scant belongings families have managed to save.
Strong winds can also topple tents and destroy families' attempts to gather food and supplies as another bleak winter sets in.
Two weeks ago, Bassil Naggar bought a new tent from the black market for 2300 NIS ($A1,093.29), because the scorching summer sun had worn his old tent thin. Still, rainwater leaked through his tent.
"I spent all (Friday) pushing water out of my tent," Naggar said, adding that his neighbours' tents and belongings were completely wrecked.
"Water puddles are inches high, and there is no proper drainage," he said
Barefoot children splashed in puddles as women made tea outside under dark clouds.
According to the UN, Muwasi, which was largely undeveloped dunes before the Israeli military designated it a humanitarian zone early in the war, held up to 425,000 displaced Palestinians this past summer, the vast majority living in makeshift temporary tents.
The Israeli defence body in charge of humanitarian aid in the Gaza Strip has said it is allowing in winter materials, including blankets and heavy tarpaulins, but aid organisations warn the efforts are far from sufficient when temperatures plummet in the winter and the wind whips off the sea.
As heavy clouds threatened further rain, some attempted to take shelter in destroyed buildings, even those at risk of collapse, with gaping holes covered by pieces of tarpaulin.
The war broke out on October 7, 2023, when Hamas-led militants launched a surprise attack on Israel, killing some 1200 people, mostly civilians, and abducting 251 hostages.
They are still holding the bodies of three hostages, which Israel is demanding in return before progressing to the second stage of the ceasefire.
Hamas has said that it is unable to locate the bodies under the rubble, but Israel has accused Hamas of dragging its feet.
The first stage of the ceasefire agreement that took effect on October 10 is nearing its end.
The next stage calls for the implementation of a governing body for Gaza and the deployment of an international stabilisation force.
It is not clear where either stands.
Israel's military campaign against Gaza has killed 69,100, including many women and children, according to the Gaza Health Ministry, which does not distinguish between civilians and combatants in its figures.
The offensive has destroyed large parts of Gaza and displaced around 90 per cent of its population of roughly two million Palestinians.
