Army, IAF and NDRF teams have been called in for rescue and relief operations. About 2,200 people have been shifted to safer places and over 460 others rescued.
In Banaskantha district, the highest recorded rainfall (342 mm) was in Dantiwada, followed by Palanpur (255 mm), Amrigadh (246 mm) and Dhanera (216 mm).
Chief Minister Vijay Rupani conducted review meetings of the situation.
He said the large inflow of water into rivers and dams in the two districts due to heavy rains in neighbouring Rajasthan made the situation worse.
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Rupani said rescue teams are ensuring that all people living in the low-lying areas are safely relocated.
"Banaskantha and Patan districts are hugely affected due to heavy rains in north Gujarat and Rajasthan. Dantiwada and Sipu dams are overflowing and due to the release of water from the dams, people living in low-lying areas have been shifted to safer places," he said.
So far, 1,526 people in Banaskantha, about 500 in Patan, and over 200 in Kalol in Gandhinagar have been shifted.
The administration is making arrangements for the distribution of food packets for affected people, the chief minister said.
The government has also decided to postpone the Narmada Mahotsav and also deferred till August 6 the Heritage Festival to be held in Ahmedabad.
According to the chief minister, in order to carry out the rescue and relief operations, more teams of the National Disaster Relief Force (NDRF) have been pressed into service.
Three helicopters of the Air Force have been kept ready in Deesa town in Banaskantha. One Army column has also been called in from Dhrangdhara.
"Sipu dam received 1.16 lakh cusecs water, and Dantiwada received 1.5 lakh cusecs," Rupani said.
As the dams overflow, water is being released, because of which people living in around 100 villages located in low-lying areas are being shifted, so that they are not hit when the water is released, Rupani said.
The water level of Banas and Sidhpur rivers is also going to rise, so relocation of affected people is being undertaken, he said.