© Motti KimchiPeople cross the road in rainy Tel Aviv
The storms raged from northern Israel to the Negev Desert in the south, and were expected to further raise the levels of the Sea of Galilee, which has already enjoyed a particularly rainy winter.
The rains were expected to continue Wednesday, but gradually peter off by evening.
The Israel Electric Corporation recorded 828 lightning strikes on Tuesday morning and afternoon, an unprecedented number for May, and up dramatically — by 2,748% — from May's monthly average of 30.
The Israel Water Authority on Tuesday said the last time the country saw two such rainy winters consecutively was over three decades ago, in late 1986- early 1988.
Last year Israel saw generous rainfall in the north, raising the level of the Sea of Galilee by 19.5 centimeters and ending a 5-year drought that plagued the area.
Parts of Highway 90 in the south were closed off to traffic Tuesday amid intermittent flooding. Strong hail was also recorded in the southern cities of Arad and Yeruham, while rains battered most cities, including Tel Aviv and Jerusalem.
Israel rarely sees rain in its dry season between April and October.
Following an especially wet winter, the Sea of Galilee in northern Israel is at its highest level in two decades. The water level came close to its all-time low in April 2017, when the level dropped to 212.95 meters (about 698 feet) below sea level. The current level is minus 208.92 meters (minus 685 feet).
Agencies contributed to this report.
Comment: A severe hailstorm also hit parts of neighbouring Saudi Arabia on May 5.