The Yamuna river here in Uttar Pradesh crossed the danger mark early Sunday, officials said.
"We are fully prepared and are closely monitoring the situation," said municipal commissioner of Agra PN Dube.
Agra drains are choked and the backflow is creating drainage problem, he said.
The Yamuna river is now flowing at the low flood level danger mark due to heavy discharges from upstream barrages, but is still below the highest levels.
The discharge from the Gokul barrage in Mathura district is increasing every few hours, following the release of water from Okhla and Hathini Kund barrages.
Hundreds of villages in Bah, Fatehabad, Etmadpur and Kiraoli tehsils in Agra are likely to be affected by the flood waters in the next few days.
The Keshi Ghat and a part of the Parikrama route at Vrindavan in Mathura are already submerged.
Police have started evacuating people from low-lying areas in Mathura.
Yamuna on Saturday submerged a large part of the Banshi-bat area in Vrindavan.
Release of more than a lakh cusecs of water Friday night has reached Vrindavan, inundating half a dozen colonies in the low-lying areas along the river bank.
Irrigation department officials said they have received reports that more than six lakh cusecs of water had been released from Tajewala barrage upstream of Delhi.