The Kenya National Highways Authority has announced the closure of a section fo Thika Road at Kahawa Sukari Drift.
The closed area is between the Kahawa Barracks and Kenyatta University.
The closure follows heavy rains that pounded the City on Tuesday night and Wednesday morning.
"Motorists heading to Thika may use Kiambu Road and turn off to Northern Bypass to Ruiru and Vice versa," KeNHA.
"The authority cautions road users against any attempts to use section if the road in the interest of their safety."
KenHA said they will continue to monitor the water levels and advise when the water levels subsides.
Many people were Wednesday morning stranded after Thika Road flooded at Kenyatta University and Juja.
Traffic flow along the Thika Super Highway was affected after a section of the highway was submerged by water, particularly the Thika bound on the underpass of the Juja Flyover area.
Motorists were using Service Lane to access the highway past the High Point area.
Also submerged are Traffic Police Offices within Juja Police Station.
Police are said to have turned away motorists on both sides of the road to avert a tragedy.
Police appealed to motorists to exercise due caution when using the Juja Super Highway.
Motor vehicles from Nairobi heading towards Thika were making u-turns and coming back to the Githurai roundabout.
No motor vehicles were heading to Nairobi from Thika.