Jhelum has crossed the 'alarm level' of 18 feet at Sangam in Anantnag district, officials said.
"We have issued the advisory after the water level in River Jhelum crossed the 18 feet mark at Sangam," a senior official of the Irrigation and Flood Control department told PTI.
He said although the water level was still rising in the river, the rate of increase had showed a downward trend in the past couple of hours.
He said the water level at noon at Sangam was 18.40 feet while at Ram Munshi Bagh in the city it stood at 15.50 feet.
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"In March 2015, a year after the devastating floods of 2014, the water level at Ram Munshi Bagh had reached 21.5 feet. So there is no need to panic yet," he added.
The 2014 floods had caused widespread destruction in the valley as more than 300 persons were killed in the deluge that struck in the month of September.
Pahalgam, also in south Kashmir, recorded rainfall of 64.2 mm of rains in the past 24 hours, the officials said.
The incessant rains have forced closure of the arterial Jammu-Srinagar National Highway as the downpour has triggered landslides and shooting stones at several places along the 300-km road.
Massive traffic jams were witnessed in many parts of the city as the road were inundated as drains were overflowing.
The divisional administration has pressed into service pumps and fire tenders to dewater the city roads.
The University of Kashmir and Islamic University have postponed all examinations for the day.
The Health Department has directed all district and block level officers to prepare for exigencies in case of flood.