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In Mount Kenya region, farmers are struggling to come to terms with the massive losses, barely weeks after some of the replanted seeds after they had fallen victim to fake fertilizers.
In Mwea Irrigation scheme, rice farms have disappeared under water.
The most affected areas of the scheme is Cumbiri, Thiba and Jambo villa where rice paddies have been destroyed.
According to Pius Njogu, a former Mwea rice mill Chairman, approximately 2,000 acres of rice plantation has been destroyed.
Njogu said the paddies were destroyed after River Thiba, which channels water for irrigation to the farms, burst its banks flowing into the plantations.
He said with each acre producing 15 bags of 90 kilogrammes of rice, the farmers concerned will literally have nothing to harvest.
"The area has lost more than 30,000 bags of paddy rice, we will produce little tonnage compared to what we have been producing," he said.
Munene Kabibu, an affected farmer, said they are yet to cost the losses.
"We are calling on the government to help us get back on our feet since the losses are massive, some of us might not afford to plant again."
In Central Imenti, Nkunjumo in Makandune location, Kaarii, Mpindi, Manthi, Karegeria and Chuura, Kathwene the scenario repeats itself.
"The farmers are suffering as large areas of farmland have been flooded," said Kiagu MCA Kiambi Ngaruni.
Ngaruni, a farmer, said most food crops had been uprooted, exposing people to the risk of hunger and loss of income.
"Our area is known for green grams, beans, maize and other crops," Ngaruni said
At Kianjai in Tigania West Josephine Kawira said her tomato farm was destroyed by the waters.
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"We use irrigation because we get higher prices for the tomatoes. My tomatoes worth about Sh80,000 were destroyed by elephants last year and this year it is the floods that have caused me losses," said Kawira.
In tea zones, several farmers in Gatanga, Kigumo and Kangema have been affected.
"This year some tea growers will deliver reduced production," said Francis Macharia, a farmer in Tuthu village.
In the Rift Valley, farmers are also counting heavy losses as a result of the floods with Perkerra Irrigation scheme, among the most affected.
The Perkerra irrigation system, considered the region's granary, was severely damaged after the Molo, Perkerra and Weseges rivers burst their banks.
Hundreds of hectares of maize crops planted by contract farmers under the Kenya Seed Company programme have been wiped out.
Joseph Sang, a farmer from Chepkanga in Uasin Gishu County attributed good maize seed germination to the ongoing rains.
In Nandi, agricultural activities have been affected adversely.
For about two months, heavy rains have affected both maize and tea subsectors. Maize farmers have been prompted to wait longer before top dressing, while weed control has remained a challenge.
Paul Kerich, a farmer in Mosop claimed he planted his crops at the onset of rains and he fears that the fertilizers would not be effective owing to floods.
Floods have also wreaked havoc in the Coast's traditional breadbasket of Kilifi, Tana River, and Taita Taveta, destroying thousands of acres of farms under maize, cassava, and beans production.
Although the Coast has not experienced rains in the recent past, rivers in Tana River, Kilifi, and Tana River have swelled and burst their banks due to heavy downpours in the upstream. Malindi Deputy County Commissioner Ms Irene Munyoki said agricultural assets, like irrigation equipment, have been damaged, a situation likely to affect crop survival and food production.
"The losses are huge. The most affected crops are maize, okra, pigweed, cassava, coconut trees, and tomatoes are underwater," said Ms Munyoki in a phone interview.
She said irrigation schemes in Garashi, Lukole, Katsangani, Paziani, Goshi, Mongotini, and Madunguni have been destroyed by the flooding, sparking fears food crisis in these areas.
"More than 10,000 acres of crops have been destroyed after River Sabaki burst its banks flooding large areas of farmland and washing away crops," said the national government administrator.
In Nyanza, Ahero and West Kano Irrigation schemes have been submerged as a result of heavy rains.
The situation at Ahero was worsened after River Nyando broke its banks last weekend, while West Kano is grappling with backflow of the lake.
Consequently, farmers said they have lost all the crops they had planted while those who were also preparing to harvest have also lost all their investments.
Authorities estimated the loss on rice farmers alone at West Kano Irrigation scheme alone at Sh50 million.
In Migori County, Winnie Malemba, chief for Nyandago Central in Nyatike said all farms in her area were affected by the floods.
Report by Marion Kithi, Renson Mnyamwezi, Phares Mutembei, Boniface Gikandi, Timothy Kariuki, Julius Chepkwony, George Sayagie, Antony Gitonga and James Munyeki, Titus Too, Martin Ndiema, Edward Kosut, Anne Atieno and Clinton Ambujo