In Rift Valley, stakeholders are scratching their heads to find a solution to the destruction left in several schools.
Walter Wanjala, the Trans Mara Sub-County Director of Education, said most schools are struggling with poor sanitary conditions.
"Our major problem is flooded pit latrines and inaccessibility of learning institutions except those near the highways," he told the Standard.
Some of those schools that have reported flooded toilets are Changina, Chepkureret, Emitiot, Olpopong, Chebulu, and Simotwet primary and secondary schools.
Those totally inaccessible are Kamermeru, Olpopongi, Sosiot, Naisukut, Cheserton, Kisiara, Kuresiet and Ndamama primary schools.
Wanjala said his office is working with the affected schools to fix the damages ahead of the school reopening.
"I have talked with the principals and head teachers from the affected schools so that we can come up with a remedy for each of the respective schools," Wanjala said.
In Nakuru County, several schools are still submerged following heavy rains.
Visoi ward MCA Hellen Chemtai said Sosiot dam in Mosop ward broke its walls and a nearby river broke its banks unleashing floodwaters to nearby farms, homes, and schools. She said Burgei's primary and secondary schools are flooded.
Joseph Lel said parents wished to have their children back to school but due to the prevailing circumstances, it will be difficult.
Joseph Chebukaka, Kuppet organising secretary, Nakuru branch, said teachers are worried about the learners going back to school.
He said River Ndarungu has swollen and children have to cross the river to access learning in over 55 schools.
"Many of our villages have been cut off and as a result, our businesses have been affected, we are worried that the area could soon run out of food supplies if the rains do not subside," Katu said.
Similarly in Western, hundreds of learners in Budalang'i and Teso North constituencies Busia County could remain confined in temporary camps when schools reopen on Monday.
According to Busia County Education Director James Ekalyio about 14 schools have been damaged by floods in Budalang'i and Teso North with at least 10,000 students likely to miss out on learning.
The affected primary schools include Bukoma, Maduwa, Bulwani, Budalaa, Musoma, and Lunyofu in Budalang'i.
In Teso North Constituency, Amoni, Kaejo, Kapkuyi, Kajei Primary Schools and Kamolo Secondary School and Kolanya Girls have been affected according to the education officer.
Ekalyio said some schools have been serving as evacuation centres. "We have more than 12 schools completely underwater in Budalangi and if the situation persists, our children will lack a place to learn from," said Elkayio.
He said UNICEF has pledged to provide tents for learning when schools reopen. "We have more than 10,000 pupils from Junior and upper secondary schools who are affected, and UNICEF has promised to help us with tents," said Elkayio.
[Report by Anne Atieno, Clinton Ambujo, Kiprono Kurgat, Julius Chepkwony, James Munyeki, Jackline Inyanji, Benard Lusigi, Robert Amalemba, Bruno Mutunga, Fayo Abraham, and Boniface Gikandi]