The nine hikers, eight female and one male, were part of a group of about 25 people who were hiking in the vicinity of the stream near the Dead Sea.
Currently one person is still missing and police volunteers and the Israeli army have formed search parties in which almost 700 people are now involved.
"We are now in a race against time to find the missing before it gets dark," said Eli Bin, the director general of the Magen David Adom medical rescue service, as reported by the newspaper Haaretz.
Israeli President Reuven Rivlin took to Twitter to express support to the families of the victims.
“Our thoughts and prayers go to our brothers, children, our loved ones, and those in danger. We're following the situation in the south closely and are sending a warm embrace to the effected families. We will strengthen and lend help to the forces who are currently working to rescue, find and treat those injured. I ask all to please follow their instructions."
Earlier on Wednesday, two teenagers were killed in flash floods near the town of Negev, as the heavy water flows continued.
The north of the country saw more breaks in the showers but was hit with very strong winds and haze.
"Twenty-five millimeters of rain fell in Tel Aviv in just one hour. This is 25 percent more than the entire average rainfall for the entire month of April in the city, 20 millimeters. Large amounts of rain also fell in Jerusalem and Beit Shemesh, 45 to 50 millimeters," Haaretz reported.