Mosquitoes’ ecology and associated arboviruses are heavily influenced by precipitation and retention of water in the environment. In 2011 and 2014, unprecedented floods occurred in Lake Baringo basin inundating approximate 88 km2 of the shoreline land. This caused abrupt environmental changes raising fears of an outbreak of Rift Valley Fever (RVF) disease. This study was carried out to determine the situation of RVF disease in livestock from diverse habitats during the extreme unprecedented flooding phenomenon that occurred in Lake Baringo basin, in 2012-2013. Blood was drawn from ear vein of livestock selected randomly from the three study areas (lakeshore land, swamp marshy and dry rangeland habitats). Mosquitoes were trapped using CDC light traps and identified morphologically. From a total of 77 blood samples, eight were positive for RVF virus (RVFV) representing an overall infection of 12%. RVF prevalence from livestock resident in flooded lakeshore land habitat was 2.6% (N=77) compared to the swamp marshy habitat at 7.8% (N=77). No infections were recorded from dry rangeland (0%). Mosquitoes of genus Mansonia dominated the catches in flooded lakeshore (98%). Highest individual catches of mosquitoes of genus Aedes was from swamp marshy area whose abundance was 96.8% and below 2% in other habitats. The Simpson’s Diversity Index for mosquitoes from swamp marshy habitat was 0.56, dry rangeland 0.57 and lakeshore land 0.13. The flooded lakeshore land was the most affected by the unprecedented floods resulting in uneven mosquito diversity and subsequently low prevalence of RVF in this habitat. This could be attributed to prolonged disruption of biotic and abiotic factors creating unfavourable breeding sites of multiple species of primary vectors of RVF in flooded lakeshore land unlike in other habitats.