The weatherman has warned that more heavy rains, which will be accompanied by strong off-shore winds resulting in storms surge in the Indian Ocean will hit the Coast region.
Fishermen, beachgoers and players in the marine sector have been asked to be on high alert.
The County Director of Meteorology Edward Ngure said that flash floods might occur in low-lying areas, places with clogged drainage and those with unfilled and abandoned quarries.
For the past one week, Mombasa residents have been grappling with heavy rains that caused heavy traffic jams especially along the highway to Nairobi, blocked and flooded roads.
"We have braved the pounding rains thinking they will subside only for the situation to get worse. Our sewers are blocked and houses are flooded. We are now scared of the eruption of waterborne diseases," Charles Kioko, a resident of Tudor said.
The weatherman has further warned that water flooded areas are breeding grounds for mosquitoes which might result in diseases such as malaria and dengue fever.
As such, health authorities have been asked to prepare to deal with such situations.
"Flash floods may lead to transport problems, especially in areas where the roads become impassable when it rains. This may inconvenience motorists and pedestrians," Mr Ngure said.
Meanwhile, Wavuvi Association of Kenya chairman Hamid Omar has asked fishermen to avoid the ocean until the weather pattern changes.
"We always take the caution seriously to avoid any mishaps. I have communicated to my colleagues to avoid high seas until the situation normalises," Mr Omar told the Nation.
The county's weather outlook shows that Mombasa will this week have light rains, increasing to moderate rains from Friday to Sunday in most places in the tourism hub.
"Cloud cover and strength of the wind is expected to increase. Maximum temperatures will reach 28 degrees Celsius. The month of May has so far recorded 182mm of rainfall up to the 18th of May. The long-term average for May is 254mm of rainfall," an outlook form the weatherman shows.
Earlier, the Mombasa County Health Department engaged in a consultative meeting with various stakeholders to discuss programmes they can develop to address public health issues currently affecting residents.
The meeting which was chaired by Chief Officer for Public Health Aisha Abubakar highlighted the areas at risk of waterborne and other diseases across the six sub-counties and the suitable interventions to address them.
The programmes include preventive practices for diseases such as diarrhoea, cholera, dysentery, malaria, dengue fever and chikungunya among other illnesses.