Boreholes are main sources of water for human use in the Rift Valley. However these boreholes have fluoride levels higher than the World Health Organization (WHO) recommended levels of 1.5 mg/l and consequently have raised serious health issues. This study sought to determine the relationship between borehole stratigraphy and fluoride levels in ground water in river Njoro catchment. This study adopted purposive longitudinal survey. The study adopted descriptive analysis of the borehole stratigraphy characteristics and fluoride levels recorded. The sources of data included; field surveys which were used to collect data on the borehole fluoride levels data and qualitative analysis of the stratigraphy data. From the results of the study, it was observed that the fluoride levels in boreholes in river Njoro catchment were dependent on the stratigraphy matrix of the boreholes. Therefore lithological formations have an influence on fluoride level River Njoro catchment. This study will form a pool of knowledge to other researchers who have an interest in the study of fluoride occurrence in ground water in the Rift Valley. Further the study will help in assisting the drillers in decision making after geological surveys of where to locate the boreholes.