Increased wet season rainfall is associated with improved water supply at point water sources and improved river flows and water reservoir levels. For piped water supply schemes with surface water intakes, this is supposed to enhance operations since there is adequate raw water unlike in the dry season where operations are interrupted due to insufficient flows. However, this is not the case in Nzoia River Basin as established by this study. As rainfall increases, drinking water production in treatment plants at Moi’s Bridge, Lumakanda and Busia water supplies decrease and vice versa. Nzoia River Basin is one of the regions that is highly vulnerable to climate variability in Kenya, hence understanding rainfall variability and trends is important for better water resources management and especially drinking water supply. This study aimed at assessing rainfall variability and trends for 3 rainfall stations in Nzoia River Basin; Leissa Farm Kitale, Webuye Agricultural Office and Bunyala Irrigation Scheme and its impact on drinking water production at Moi’s Bridge, Lumakanda and Busia water supplies treatment plants. The rainfall data used in this study covers 31 years period from 1970 to 2001 and was obtained from the Kenya Meteorological Department (KMD), Nairobi, Kenya. Monthly water supply production data for Moi’s Bridge, Lumakanda and Busia water supplies covering 15 years period from 2000 to 2014 was obtained from the County governments of Uasin Gishu, Kakamega and Busia. Rainfall variability and trend was analysed using the parametric test of Linear regression analysis and the non-parametric Mann Kendall statistical test. Monthly rainfall and monthly drinking water production was analysed using Pearson moment correlation to establish the relationship between monthly rainfall and monthly drinking water supply production at Mois Bridge, Lumakanda and Busia Water supplies treatment plants. The results of variability and trend in annual rainfall shows Webuye Agricultural Office recording declining rainfall at -0.8994 mm/31 years (-0.029 mm/ year); whereas Leissa Farm Kitale shows increasing rainfall at 1.0325 mm/31 years (0.033 mm/ year) and Bunyala Irrigation Scheme’s rainfall is increasing at 0.5245 mm/31 years (0.017 mm/ year). Drinking water supply production at Moi’s Bridge, Lumakanda and Busia water supplies has been increasing with time between 2000 and 2014. The results of Pearson moment correlation coefficient shows a strong negative relationship between monthly rainfall and monthly drinking water supply production at 0.05 significance level for Moi’s Bridge, Lumakanda and Busia water supplies. This shows that as rainfall increases, drinking water supply production in treatment plants at Moi’s Bridge, Lumakanda and Busia water supplies decreases. During the rainy season, the cost of water treatment goes up as a result of increased turbidity. Increased rainfall in Nzoia River Basin presents water treatment challenges to the existing water supply treatment plants resulting into reduced production.Water supply managers should improve the capacity of the existing water supply treatment plants to cope with the increased rainfall variability under the changing climatic conditions.