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Lakes Baringo and Bogoria are now just seven kilometres apart as rising water levels raise fears that the two could merge, threatening the region's ecosystems and communities.
The Government has begun emergency drainage works to control water flows around the lakes and prevent further flooding in Baringo County.
Principal Secretary for Irrigation Ephantus Kimotho inspected the ongoing works on Saturday, as engineers began restoring Rivers Loboi and Waseges to their original drainage courses.
The distance between the two lakes has reduced from about 22 kilometres a decade ago to seven kilometres, raising concerns that Lake Baringo's freshwater could mix with the alkaline waters of Lake Bogoria.
Such a connection could alter the ecological balance of the two lakes and affect surrounding ecosystems.
Data presented during a technical briefing show that Lake Baringo's water volume has increased by an estimated 1.4 billion to 1.9 billion cubic metres by 2026.
The lake's water level has also risen by between 12 and 14 metres, from 972 metres to about 984 metres above mean sea level.
Before 2010, the lake covered between 108 and 130 square kilometres, depending on seasonal changes.
The rising water has submerged agricultural land, displaced communities and damaged infrastructure.
Kimotho said the immediate intervention would focus on restoring the natural flow of Rivers Loboi and Waseges through river training, desilting and removing accumulated sediments.
Technical assessments have linked changes in river drainage patterns and increased water inflows to rising water levels in Lake Bogoria.
The Government also plans to improve drainage channels to manage excess water and facilitate its controlled movement from Lake Baringo.
Beyond the emergency works, the Government plans to invest in water storage facilities, irrigation infrastructure, canals and check dams to turn the flooding challenge into an economic opportunity.
Preliminary assessments have identified potential to develop 250,000 acres for irrigation, with an initial target of 100,000 acres subject to feasibility studies.
The proposed programme aims to expand food production, support livestock development, create jobs and increase household incomes in communities that depend on livestock keeping and small-scale farming.
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More than 96 residents have secured jobs through the ongoing works, undertaking river clearance, excavation, plant operation and other construction activities.
Irrigation Secretary for Programmes Michael Thuita leads the multidisciplinary engineering team overseeing the interventions.
Kimotho was accompanied by Secretary for Administration Yatich Kipkemei, Irrigation Secretary for Land Reclamation, Climate Resilience and Irrigation Water Management Joel Tanui and national and county government officials.
The Government says the interventions will combine flood management, environmental protection and irrigation development to protect communities and support agricultural production in the Baringo region.