Recent trends show that in the coming decades, Kenya’s natural resources will continue to face significant pressure due to both anthropogenic and natural stressors, and this will have greater negative impacts on socio-economic development including food security and livelihoods. Understanding the impacts of these stressors is an important step to developing coping and adaptation strategies at every level. The Water Towers of Kenya play a critical role in supplying ecosystems services such as water supply, timber and non-timber forest products and regulating services such as climate and water quantity and quality. To assess the vulnerability of the Water Towers to climate change, the study adopted the IPCC AR4 framework that defines vulnerability as a function of exposure, sensitivity, and adaptive capacity. The historical trends in rainfall indicate that the three Water Towers show a declining rainfall trend during the March-April-May (MAM) main rainy season, while the October-November-December (OND) short rainy season shows an increase. The temperature patterns are consistent with the domain having a common rising trend with a rate in the range of 0.3˚C to 0.5˚C per decade. Projection analysis considered three emissions scenarios: low-emission (mitigation) scenario (RCP2.6), a medium-level emission scenario (RCP4.5), and a highemission (business as usual) scenario (RCP8.5). The results of the high-emission scenario show that the annual temperature over the Water Towers could rise by 3.0˚C to 3.5˚C by the 2050s (2036-2065) and 3.6˚C to 4.8˚C by the 2070s (2055-2085 results not presented), relative to the baseline period 1970- 2000. The findings indicate that exposure, sensitivity, and adaptive capacity vary in magnitude, as well as spatially across the Water Towers. This is reflected in the spatially variable vulnerability index across the Water Towers. Overall vulnerability will increase in the water towers leading to erosion of the resilience of the exposed ecosystems and the communities that rely on ecosystem services these landscapes provide.