In the face of climate change, a number of climate variables such as temperature, precipitation, wind speed, humidity and solar radiation tend to affect water resources. This has led to changes in soil moisture, reduced stream run off, reduced ground water recharge and increased transpiration which ultimately causes deterioration of on-farm water resources. Deteriorating water resources at farm level as a result of climate change has led to decreased crop yields in sub Saharan Africa and threatens food security, livelihoods as wells as water security. Understanding factors affecting farmers’ perception of climate change effects on water resources is key in informing policies that can transform smallholder agriculture in Africa to be more resilient to the effects of climate change. This study assesses farmers’ climate change perceptions on water resources at farm-level in Kakamega County, Kenya. Using data collected from 159 farm households in Kakamega County, ordered probit was employed to assess factors affecting farmers’ perception of climate change based on water resources. The results indicate that gender, farm size, distance to the main water source, extension services, access to climate change information through radio and wealth status significantly explained levels of farmers’ perception of climate change based on water resources. The findings inform policies aimed at increasing awareness of climate change effects on on-farm water resources and consequently enhance adaptive water management strategies among smallholder farmers.