Nabil Taha, 45, was stuck with his minibus and his 11-year-old son, Ali, north of the riverbed.
They had tried to get to their home in the town of Rafah on Thursday evening, but were stopped by the flood.
Taha said: "When we crossed the first time, the waters weren't too high, but when we tried to get back across we couldn't."
They spent the night in the minibus, he said.