Groundwater is used extensively in the Central Kenya Rift for domestic and agricultural demands. In these active rift settings groundwater can exhibit high fluoride levels. In order to address water security and reduce human exposure to high fluoride in drinking water, knowledge of the source and geochemical processes of enrichment are required. A study was therefore carried out within the Naivasha catchment (Kenya) to understand the genesis, enrichment and seasonal variations of fluoride in the groundwater. Rocks, rain, surface and groundwater sources were sampled for hydrogeochemical and isotopic investigations, the data was statistically and geospatially analyzed. Water sources have variable fluoride concentrations between 0.02–75mg/L. 73% exceed the health limit (1.5mg/L) in both dry and wet seasons. F− concentrations in rivers are lower (0.2–9.2mg/L) than groundwater (0.09 to 43.6mg/L) while saline lake waters have the highest concentrations (0.27–75mg/L). The higher values are confined to elevations below 2000masl. Oxygen (δ18O) and hydrogen (δD) isotopic values range from −6.2 to +5.8‰ and −31.3 to +33.3‰, respectively, they are also highly variable in the rift floor where they attain maximum values. Fluoride base levels in the precursor vitreous volcanic rocks are higher (between 3750–6000ppm) in minerals such as cordierite and muscovite while secondary minerals like illite and kaolinite have lower remnant fluoride (<1000ppm). Thus, geochemical F− enrichment in regional groundwater is mainly due to a) rock alteration, i.e. through long residence times and natural discharge and/or enhanced leakages of deep seated geothermal water reservoirs, b) secondary concentration fortification of natural reservoirs through evaporation, through reduced recharge and/or enhanced abstraction and c) through additional enrichment of fluoride after volcanic emissions. The findings are useful to help improve water management in Naivasha as well as similar active rift setting environments. Display omitted •Rocks and water samples from the Central Kenya Rift, were analyzed for F−.•73% of water sources are above the NEMA health guideline (1.5mg/L) on fluoride.•Fluoride concentration is highly variable in waters in the rift (0.22–74.98mg/L).•Minerals (cordierite, muscovite, villiaumite) have high fluoride 308–6366ppm.•Fluoride enriches in water by rock alteration, evaporation and geothermal mixing.