The heavy downpour started in the wee hours and continued for the better part of Saturday.
The downpour left many roads and streets flooded.
Residents took to social media to express their disappointment at the condition of the roads and posted advisories to apprise people of the situation.
The heavy rains also caused street flooding and congestion in most parts of Mombasa and left stall owners along the Mombasa-Kwale highway counting after flood waters swept their structures.
Traders blamed the problem on to lack of proper drainage as the water did not recede in most low-lying streets causing traffic in the town centre for the better part of the day as the rains continued intermittently.
Areas such as the Central Business District, Likoni, Kisauni, Changamwe and Jomvu were affected by the floods due to heavy rains that have been pouring down the city for hours on end.
Sections of Muslims in Mombasa that have held Eid-al-Fitr prayers marking the end of the holy fasting month of Ramadhan were forced to offer the special prayers in mosques and community halls instead of open grounds and stadiums.
Despite the heavy downpours, Muslims came out in large numbers to attend Eid prayers.
Residents have expressed their anger and lamented at how properties were destroyed due to the rainwater entering the homes and business premises.
A spot check in low-lying areas shows that residents bore the brunt of the flooding and remained indoors for the better part of the day.
Roadside traders said flooding swept away their structures and stalls and the few that remained standing were waterlogged.
The heavy downpour that has caused havoc in different parts of the port city has also resulted in vehicular traffic.
The weather service last week issued an advisory that heavy rain of more than 30mm is expected in various parts of the coastal strip and that fishermen were asked not to venture out.
I shouldn't laugh, but their dusty godforsaken place of inhabitance is about to become increasingly wet, very wet.