Learning in the Nyanza region has been disrupted and transport paralysed in some areas as heavy rains left schools flooded and some roads cut off after bridges collapsed.
Many learners are unable to access their schools while the few who have been reporting have been sent back home.
Transport services were paralysed in parts of Siaya, Migori and Homa Bay counties after key bridges were washed away by floods following a heavy downpour.
St Paul Nyamasao Primary, Ogenya Primary in Nyando, and St Marks Nyabera and Kasagam schools in Kisumu East are some of those that have been affected.
St Paul Nyamasao Primary School head teacher Hosea Nunda told the Nation the backflow from Lake Victoria started filling the school compound on Tuesday afternoon.
"We had to send the children back home though the teachers are still in the staff rooms," said Mr Nunda. He added that by Tuesday, 150 learners out of 450 had not reported to school.
According to Kakola-Ombaka location assistant chief Jacob Ongudi, many families have been displaced.
"About 1,800 families have been forced to move and seek shelter in churches around," he said.
By Sunday, Nyando residents had started moving to higher grounds. The most affected areas are Kasiwidhi South, Kaloo South, Kanyipola South and Kasambula Kosawa.
Mr Ongudi appealed to the county government and well-wishers to step in and provide relief food, medical aid and non-food items for the flood victims.
In Migori, pupils in Angugo, Kabuto and Nyora primary schools in Nyatike sub-county failed to report as schools reopened for third term due to the floods
The ongoing heavy downpour has seen over 800 families left homeless for close to a month weeks after Kuja river broke its banks, flooding several villages . Compounded by the backflow from Lake Victoria, Angugo, Nyora, Modi and Lwanda villages are inhabitable.
Transport services were cut off between Kanyamkago in Migori County and Kanyikela in Homa Bay County after a bridge that connects the two areas collapsed. The Oria-Riat bridge on Kuja river collapsed on Wednesday morning. No casualties were reported.
Migori County Commissioner Boaz Cherutich said a team comprising the Red Cross, education officials and local administration had been dispatched to assess the situation.
"We are planning to relocate the pupils to neighbouring schools," he said.
In Siaya, the Dhogoye Bridge connecting Bondo Usenge and Osieko was washed away by floods. The Kenya National Highways Authority (Kenha) sent out a travel advisory following the increased rainfall.
"Since there is no alternative access to Osieko, we wish to advise motorists along that section not to attempt crossing the overtopped section and to only cross when the water levels are low," read the tweet.
"The water has already covered the road, we fear that if the rains continue the Lake Victoria water will spread to River Yala and the road will be no more," said George Omondi, a resident of Nyangera in Usenge.
Kenha also warned heavy trucks to avoid using the crossing for now as they evaluate mechanisms of undertaking works on the structure.
"A permanent bridge is planned and procurement process is underway to solve the rising Lake Victoria water levels at this crossing," read the statement.
In Busia, hundreds of families in Bunyala sub-county have been moved to higher grounds following floods occasioned by the Lake Victoria backflow and River Nzoia, which has broken its banks.
More than 800 families have been relocated to camps on safer grounds by the government.
"We are expecting more families to move as the downpour increases," said Bunyala Deputy County Commissioner Grace Ouma.
Report by Elizabeth Ojina, Rushdie Oudia, George Odiwuor, Ian Byron and Shaban Makokha