The Mumbai-Agra highway in Gwalior was badly affected and vehicles are now being stopped at several points.
Due to heavy discharge by the Kota Barrage, the Chambal is close to the danger mark in Morena, Dholpur.
Police said river water is now entering fields.
Another river in the region, the Uttangan, is also on the rise cutting off many villages on the Rajasthan border with Agra.
Though the Yamuna level in Mathura and Agra was still a few metres below the low flood danger level, officials are on the vigil and have asked people to be prepared to evacuate if the water level crosses the danger mark Monday.
Several spells of heavy showers Saturday and Sunday affected not only traffic mobility but also cut off some villages.
The situation was worsened by illegal sand mining along the Yamuna banks.
Agra's annual rainfall average of 650 mm has already been equalled, "so what comes now till September will be a bonus for this area", said progressive farmer Ravi Singh.
Another witness, Bishal Dev Rishi, after a tour of the region, said the Yamuna was flowing to the brim and "afforded such a spectacular view along the 101 Shiva temples in a row. It's breath-taking".
Meanwhile, there were long queues of vehicles along the NH-3 near Saiyyan on the Gwalior road, waiting anxiously for the water level to recede to be able to cross the Chambal bridge.
"The memories of 1996 are still fresh, when the bridge came tumbling down," said truck driver Anand Kumar.
Irrigation department officials said there has been huge discharge of water from Gandhi Sagar and Kota barrages, and by Monday the water should reach Pinahat and flood dozens of villages.
--IANS (Posted on 12-08-2013)