Before the most recent floods, Mr Sakaja had defended the development of high-rise buildings in some residential areas, saying the only way Nairobi would develop was to build up.
His stance had come amid criticism that the developments were straining an already overwhelmed infrastructure. He has now issued a directive stopping all building development approvals "until we can review all those that have been issued and are continuing in the city".
A number of MPs also criticised the governor over city management, citing the sewage and flooding crisis.
Mr Sakaja has defended himself, saying the criticism was politically motivated.
Outspoken Senator Samson Cherargei from the ruling coalition said the governor was not to blame as "the problem we are having begun in 1963, you cannot resolve it now".
Some of the problems can be traced back to the origins of Nairobi - meaning a "place of cool waters" in the Maasai language - and the fact that it was not considered a suitable place for large numbers of people to live in.
It started as a railway depot under the British colonial authorities in the late 1890s. The engineers who worked on the site called the area a "swamp", with soggy land and "unsanitary conditions".
Years later, colonial official Sir Charles Eliot said Nairobi sat in "a depression with a very thin layer of soil or rock. The soil was water-logged during the greater part of the year".
Nevertheless, the city developed into an attractive city with good weather, a lot of greenery and a national park.
But its drainage problem has persisted.
An initial masterplan by the colonial authorities took into consideration the lay of the land and designed measures to prevent disasters. There have been at least two other blueprints post-independence to date - but they have mostly not been implemented.
This season's floods show that as rainfall could get more intense as a result of climate change a new plan is urgently needed, Prof Omenya said.
But the ordinary city-dweller is left mopping up, hoping that the rains subside.